Posterb presentations Đề tài nghiên cứu về cây lúa

IRC14-0370
01a. Ex situ conservation and dissemination of rice germplasm
SHOULD THE GENEBANK STANDARDS FOR SEED DRYING PRIOR TO LONGTERM
STORAGE BE CHANGED?
K. Whitehouse1, F. Hay2, R. Ellis1
1
Agriculture Policy and Development, University of Reading, Reading, United Kingdom
2
Genetic Resources Center, International Rice Research Institute, Los Banos, Philippines
Purpose:
Despite remaining several decades under genebank storage conditions, over time seed viability
declines and regeneration is required to maintain genetic integrity. While recommendations for the
management of genebank accessions emphasise the importance of seed drying to extend
subsequent seed longevity during storage, there has not been a critical evaluation (impact on
subsequent quality / longevity of the seeds) of the conditions that are actually used by genebanks
for any species.
Approach and methods used:
Seed storage experiments were used to evaluate the relative longevity of seeds of 20 diverse rice
accessions (representing five variety groups), following initial drying in a dry room (DR) running
within recommended genebank conditions (15% RH, 15°C), or using heated air (45°C) in a flat-bed
batch dryer (BD). Seed longevity under real-time genebank storage was estimated by extrapolation
from the results of the seed storage experiments.
Key results:
The initial rate of drying did not appear to differ between the different drying methods, however
initial drying in the BD resulted in significantly greater subsequent longevity compared with initial
drying in the DR for 14 accessions, with the difference in longevity (as measured by the time for
viability to fall to 50%; p50) as a percentage of the p50 of seeds initially dried in the DR. Initial drying
for a single daily cycle (8 hours) in the BD compared with drying in the DR never had a negative
effect on subsequent longevity. There were significant (P < 0.01) linear relationships between the
percentage difference in p50 (BR/DR) and each of harvest date, harvest moisture content and the
p50 of DR seeds, but not with maturity (days after anthesis) of the seeds at harvest.

Synthesis and Applications:
IRRI currently regenerates over 4000 accessions annually; this figure could potentially be reduced
due to the greater longevity of rice accessions if IRRI were to routinely use the BD for drying
accessions regenerated at IRRI.
Beyond IRRI, if similar results are obtained from, in particular, other cereal species, it may be
necessary to change the current genebank standards for drying to ensure seeds have maximum
longevity when they are first placed into storage.


IRC14-0445
01a. Ex situ conservation and dissemination of rice germplasm
PHYSIOLOGICAL AND GENETIC CHANGES IN RICE (ORYZA SPP) SEEDS DURING AGEING
K.A. Adeboye1, I.O. Daniel1, J.G. Bodunde2, M.A. Ayo-Vaughan1, J.A. Adetumbi3, E.O. Idehen1,
O.W. Adabale1
1
Plant Breeding and Seed Technology, Federal University of Agriculture Abeokuta, Abeokuta,
Nigeria
2
horticulture, Federal University of Agriculture Abeokuta, Abeokuta, Nigeria
3
grain legumes improvement programme,
Institute of Agricultural Research & Training PMB 5029 Moor Plantation, ibadan, Nigeria
Purpose:
Seed deterioration in terms of viability and vigour has implications on erosion of variability in
genetic resources especially in gene bank seed collections. This study was conducted to evaluate
physiological and genetic integrity of rice seeds during storage in a controlled deterioration
experiment.
Approach and methods used:
Ten accessions of rice sourced from the gene bank of National Centre for Genetic Resources and
Biotechnology (NACGRAB) Ibadan, Nigeria, were subjected to artificial ageing. The procedure

involved storing the seeds at 45°C and 75% Relative Humidity in a chamber. Samples of three
replicates of 20 seeds each were randomly drawn from the chamber at 0, 3, 24, 48, 55 and 72
hours. These samples were subjected to standard germination tests and DNA analysis. Data were
collected on seed germination count, percentage germination and seedling length. Seed
germination rate and vigour index were estimated. Genetic changes during ageing were evaluated
by Simple Sequence Repeat (SSR) analysis using 5 DNA primers in a Direct PCR kit. All
experiments were Completely Randomised and percentage germination data were subjected to arc
sine transformation and Analysis of Variance. Seed longevity data were subjected to Probit
analysis and genetic profiles were analysed by estimating probability of genetic drift using Nei’s
formula. Genetic distances were estimated using PASTTM software and percentage genetic
integrity was estimated from the genetic distance matrices.
Key results:
A progressive decline was observed in the viability and seedling vigour index and were maximal at
72 hours of ageing with seed viability value for all accessions averaging 54.25%. Probit analysis
revealed that NERICA 1 had the best storage potential (P50 = 82 hours) compared with other
accessions. Variation observed in the genetic integrity was revealed by primer RM 178, which
showed significant probability (p < 0.05) of genetic drift for all the accessions. Percentage genetic
integrity calculated ranged from 99.45 in NERICA 1 to 100 in IR 64 and deterioration was maximal
at 72 hours of ageing when percentage seed germination was 54.25.
Synthesis and Applications:
In order to maintain optimal genetic integrity during storage, a seed viability benchmark of 54% is
recommended for regeneration of stored rice seeds.


IRC14-0552
01a. Ex situ conservation and dissemination of rice germplasm
ASSESSMENT OF VIABILITY, GERMINATION POTENTIAL AND DORMANCY BREAKING
METHODS OF SRI LANKAN ENDEMIC WILD RICE SPECIES ORYZA RHIZOMATIS.
G. Rajkumar1, J. Weerasena2, K. Fernando3, Y. Liyanage4
1

Department of Botany, University of Jaffna, Jaffna, Sri Lanka
2
Institute of Biochemistry Molecular Biology and Biotechnology, University of Colombo, Colombo,
Sri Lanka
3
Agricultural Biotechnological Centre, University of Peredeniya, Kandy, Sri Lanka
4
Seed Testing Laboratory, Deaprtment of Agriculture, Kandy, Sri Lanka
Purpose:
Oryza rhizomatis is an endemic wild rice species of Sri Lanka. Seeds of O. rhizomatis may have a
special structure and dormancy to tide over unfavorable conditions of dry zones of Sri Lanka.
Studies carried out to findout prediction of viability, germination and dormancy breaking methods
for the seeds of O.rhizomatis. Commercial cultivated variety Bg352 was used as a control.
Approach and methods used:
The experiments were carried out on pure seeds. Four hundred seeds from each seed lot were
used for viability, dormancy breaking and germination test with eight replicates of 50 seeds and
these were subjected to various treatments separately. The seeds were soaked in distilled water
for 3-18 hours before staining and a cut was made through the middle of the embryonic axis of the
seeds. The seeds were immersed in 1% TZ solution. These were incubated in darkness for 2-36
hours for the viability test. Viability of each seed was interpreted according to the topographical
staining pattern of the embryo and the intensity of the colouration. Heat, mechanical and chemical
treatments were done to break the dormancy of seeds. The germination of O. rhizomatis was
tested using germination boxes containing sterile soil. First and the final counts were taken after 5th
and 14th days respectively by visual observation. Germination and the mortality rates were
calculated.

Key results:
O. rhizomatis seeds used in the study were found to be 80% viable. However, only 5% of seeds
germinated under the optimum laboratory conditions. From this study, it was confirmed that O.
rhizomatis seeds are dormancy thus proper treatments are required to break the dormancy as

compared to Bg352. Experiments carried out to break dormancy showed that seeds subjected to
heat treatment at 50oC for 96 hours followed by removing husks and soaking them in 0.1 M HNO3
for 24 hours increased the germination up to 76%.

Synthesis and Applications:
Therefore, these studies provide rapid, effective and valuable techniques for prediction of seed
viability, breaking of dormancy and for optimum germination of the seeds of O. rhizomatis. The
present studies will pave the way for successful cultivation and multiplication of this species, which
is crucial for varietal development.


IRC14-1056
01a. Ex situ conservation and dissemination of rice germplasm
GENETIC DIVERSITY OF IRANIAN RICE GERMPLASM THROUGH AGRO-MORPHOLOGICAL
TRAITS
M. Jahani1, M.H. Fotokian2, B. Nakhoda3, G. Mohammadi-Nejad4
1
agronomy and plant breeding, Shahid Bahonar University of Kerman, Kerman, Iran
2
agronomy and plant breeding, Shahed University, Tehran, Iran
3
Department of molecular physiology, Agricultural Biotechnology Research Institute of Iran, Karaj,
Iran
4
Plant Breeding, Shahid Bahonar University of Kerman, Kerman, Iran
Purpose:
Genetic diversity constitutes the raw material for plant improvement, and provides protection
against genetic vulnerability to biotic and abiotic stresses. Iran has diverse agronomic landscape
and potentially preserves high level of genetic resources for rice genotypes. The major objective of
this study was to quantify genetic diversity of Iranian rice genotypes

Approach and methods used:
Morphological characterization of 36 rice genotypes using 17 agro-morphological traits was done in
a field experiment by a lattice design with 3 replication. Analysis of variance, Cluster analysis and
principal component analysis were carried out
Key results:
Analysis of variance showed that the differences among genotypes for all the characters under
study were highly significant, indicating that the genotypes were highly diversified. PCA
components explained 87.86% of variation.The clustering pattern clearly grouped the genotypes
based on their originality, breeding variety, genotypes, landraces and conventional variety
generally were clustered into the different groups or subgroups.
Synthesis and Applications:
The importance of the conservation in on-farm landraces of Oryza Sativa and its wild relatives was
proposed in order to ensure the genetic resources for further breeding and conserve biological
diversity.


IRC14-1122
01a. Ex situ conservation and dissemination of rice germplasm
CAN CHLOROPHYLL FLUORESCENCE BE USED TO DETERMINE THE OPTIMAL TIME TO
HARVEST RICE SEEDS FOR LONG-TERM GENEBANK STORAGE?
S. Timple1, F.R. Hay1, B. van Duijn2
1
T.T. Chang Genetic Resources Center, International Rice Research Institute, Los Baños,
Philippines
2
Leiden University, Institute Biology Leiden and Fytagoras, Sylviusweg 72 2333 BE Leiden,
Netherlands
Purpose:
The study aims to examine the potential use of chlorophyll fluorescence (CF) to determine the
optimal time to harvest rice seeds for maximum longevity in genebank storage.

Approach and methods used:
Twenty rice accessions from the International Rice Genebank (IRG) at IRRI were planted during
the 2013 dry season and harvested at 24, 31, 38 and 45 days after peak flowering. After threshing
and drying, half of each seed lot was hand-sorted by genebank staff. Comparative longevity
experiments were conducted with and without hand-sorting at 10.9% moisture content and 45°C.
Samples were taken every 3 days for up to 60 days for viability monitoring through a standard
germination test and the time for viability to fall to 50% (p50), as a measure of seed longevity,
determined. Hand-sorted and non-sorted samples of the seed lots were subjected to CF analysis
using the SeedAnalyser.
Key results:
Seed longevity generally increased during seed development, with p50 increasing by between 42.8
and 348.6% between the first and last harvest. CF curves (number vs. pico-amps) showed distinct
peaks but were significantly skewed. The position of the peak and area under the curves (total CF)
varied with accession, maturity and whether or not the seeds had been manually sorted. Total CF
was generally highest in the least mature seeds and decreased with increasing maturity (by
between 0.25 and 6.30%, depending on accession). The position of the peak shifted downwards by
between 60 and 1050 pA as maturity increased between 24 and 45 DAF.
Synthesis and Applications:
Harvesting seeds at optimum maturity is extremely important to obtain seeds of high quality with
maximum potential longevity. It is therefore essential to have an effective and reliable technique to
be able to determine optimal harvesting time of rice seeds for conservation in long-term storage.
Based on the CF and comparative longevity results, the potential use of CF to improve genebank
operations will be discussed.


IRC14-1291
01a. Ex situ conservation and dissemination of rice germplasm
USE OF FUNGICIDES AND RELATIONS WITH THE QUALITY AND CONSERVATION OF RICE
SEEDS
I.S.N. Dario1, A.D.L.C. Novembre1

1
Crop Science, Universidade de São Paulo, Piracicaba, Brazil
Purpose:
Brasil is the 9th largest producer of rice and the first outside Asia, with production of 12.3 million
tons in 2013/14 harvest and productivity of 7.0 ton/ha in irrigated areas. The incidence of disease is
a major factor affecting rice production in Brazil and the seed treatment with fungicides is a recent
study. This research has the purpose to evaluate the interference of fungicide application on the
quality of rice seeds, according to the enviroment and period of storage.
Approach and methods used:
The experiment was developed at the Laboratory of Seeds Analysis, Crop Science Department,
Universidade de São Paulo, Piracicaba, Brasil. The research consisted of 72 treatments and 4
repetitions: nine seed lots of three important cultivars of rice produced in Brazil, treated with the
fungicides Penflufem + Trifloxystrobin, Thiabendazole + Metalaxyl + Fludioxonil and Pyraclostrobin
+ Thiophanate-methyl + Fipronil, at doses of 50, 100 and 150 ml / 100 kg seed of rice, respectively,
having a control without treatment, these seeds were stored for 120 days in two environments:
natural and dry cold room (10 °C and 20% RH). The seeds were evaluated 1, 15, 30, 60 and 120
days after treatment. To determine the seed quality were evaluated water content, germination,
vigor (first count of germination, seedling length, accelerated aging and cold tests) and sanity. The
experimental design was completely randomised, with analysis of variance for each cultivar and
comparison of average by Tukey test (5%).
Key results:
The results indicate: a) There is the influence of the fungicide, the environment and the storage
period on rice seeds quality; b) The fungicide interference on the rice seeds quality varies
according to the cultivar; c) Fungicides are efficient for the control of major pathogenic fungus
associated with rice seeds.
Synthesis and Applications:
It is vital that the rice seeds are stored in period and environment appropriate to maintain their
quality for a longer period of time, and are treated with fungicides to ensure their sanity, preventing
the spread of disease in producing areas.

IRC14-1361
01a. Ex situ conservation and dissemination of rice germplasm
THE INTERNATIONAL RICE GENEBANK: RECENT DEVELOPMENTS IN MANAGING THE
WORLD RICE COLLECTION
F. De Guzman1, R. Reano1, M.S. Almazan1, G.L. Capilit1, N.R. Sackville Hamilton1
1
TTC Genetic Resources Center, International Rice Research Institute, Los Baños, Philippines
Purpose:
The International Rice Genebank (IRG) at IRRI, having more than 121,000 available accessions,
holds the largest and the most diverse collection of rice genetic resources. The search,
development and implementation of best conservation strategies have been the utmost priority of
IRG to maximize the storage life, maintain genetic integrity, and ensure availability of high quality
seeds and information of the collection.
Approach and methods used:
IRG, through the support of the Global Crop Diversity Trust (GCDT) is continuously renovating its
facilities and improving protocols. The Seed Physiology section with modern equipment was
established to conduct research to optimize procedures and practices focusing on seed
development, drying, storage and dormancy.
New applications and modifications were added to the Genetic Resources Information
Management System (GRIMS) to cope with the improvement in protocols. It was linked to the
International Rice Information System (IRIS) for better documentation, genealogy and germplasm
tracking. The genebank has implemented the use of barcoding and Android technology not only for
precise inventory of stocks and accurate seed dissemination but also for efficient paperless data
collection for plant monitoring and characterization activities.
Biosystematic studies are being done to verify relationship between and among species, and
molecular research activities are conducted to enhance germplasm utilization.

Key results:
The improvements in facilities and procedures, and shift to automated data collection resulted to a

more efficient and cost effective conservation, regeneration, characterization and distribution
strategies to handle the increasing collections (e.g. GCDT regeneration and Gatsby collection
projects, genetic stocks) and requests. The collection is now more secured with approximately 98%
backed up at National Center for Genetic Resources Preservation (NCGRP) and Svalbard Global
Seed Vault (SGSV).

Synthesis and Applications:
The recent genebank developments have greatly helped in managing the huge collection and
facilitated the seed distribution process. These various activities and strategies undertaken by IRG
have mitigated identified risks in the conservation of rice genetic resources as well as assured the
general public and germplasm owners of the availability of quality seeds and information.


IRC14-0057
01b. In situ conservation of wild rices
ASSESSMENT OF MORPHOLOGICAL DIVERSITY WITHIN WILD RICE (ORYZA RUFIPOGON
GRIFF.) GERMPLASM OF NBU CAMPUS (WEST BENGAL) FOR IN SITU CONSERVATION- A
CASE STUDY.
S. Roy1
1
Department of Botany, University of North Bengal, Siliguri, India
Purpose:
Population of Oryza rufipogon Griff. (Poaceae) have been gradually reduced due to ecological
stresses. It has proven to be a valuable reservoir of genes for rice genetic improvement as a
progenitor of cultivated rice (O. sativa L.). It needs immediate attention with high priority so that we
could not loss this agriculturally important Oryza gene pool.
Approach and methods used:
Natural population of Oryza rufipogon in the North Bengal University campus is characterized
based on phylogeographic and morphological parameters for conservation purposes. Twenty-five
plants were considered randomly to measures twenty-six different types of morphological passport

data for genetic relatedness analysis within the population. Diagnostic characters are provided to
delineate the species morphologically.
Key results:
Plant is annual ecotype having culms height 64 cm -145 cm. Profuse fibrous roots of 2 mm thick
and 3 – 9 cm long creamy-white in colour grows from the floating nodes, node region is solid and
pinkish in colour (5-7 mm long). Flag leaf length ranges from 13 cm – 40 cm with 0.3 cm – 1.8 cm
width. Flag leaf blade attitude is varying from deflexed to horizontal to semierect. Auricle was hard,
curved and 13 – 15.5 mm in size. Two-cleft ligule length ranges 17 mm to 35 mm. Panicle length
varies from 15.4 cm – 30 cm with 1 cm – 8 cm wide with 5-13 primary branches. Attitude of primary
branches is spreading, well-exserted (100%), alternately arranged on the wavy axis. Length of the
lemma varies 6-11 mm and 1.4 – 2.3 mm wide, lemma-awn junction marked by a pinkish
pubescent constriction with 23 – 80 mm long red awn. Yellow colour anthers vary in length 4-8 mm
long. Stigma was bifurcated (> 2 mm) and purple in colour comes out from the spikelets. Seeds
(blackish) are harvested during November-December and vary in length (7.5 mm – 10 mm).
Density of fertile spikelets ranges from 15 to 82. Grain length/breadth ratio was 3.73 (average) and
average kernel length/breadth ratio was 3.99.
Synthesis and Applications:
The results suggest that the population of NBU campus are genetically diversified, heterogeneous
and should be conserved in situ to protect this precious genetic resource as separate ecological
race (ecotype or intergrade) for germplasm enhancement.


IRC14-0080
01c. Conservation and use of traditional varieties (incl. on farm conservation)
CONSERVATION OF AROMATIC RICE BIODIVERSITY: HERITAGE OF BANGLADESH
M. Salam1, M. Islam1, P. Saha1
1
Agriculture and Food Security, BRAC, Gazipur, Bangladesh
Purpose:
Small grain aromatic rice landraces are the thousand year’s tradition of Bangladesh. Because of

many aristocratic dishes viz. Polao, Berani, Firny and Payesh are prepared from this group of rice
varieties. Serving those prestigious foods to dignitaries, guests and ceremonial functions is a
Bangladeshi culture. But the cultivation of these varieties has been progressively diminishing due
to their low yields and photoperiod sensitivity that restrict their production to the wet season.
Recently, several media reports reflected concerns of the risk of extinction of this precious
heritage. Therefore, efforts have been taken to collect and conserve these cultivars to maintain rice
biodiversity.
Approach and methods used:
Nationwide field collection was done by village level staff of BRAC. Accessions were assembled
from BRRI gene bank and Bangabandhu Sheikh Mujibur Rahaman Agricultural University and 154
genotypes were grown at BRAC farm, Gazipur, during Aman season of 2013. Twenty five days old
seedlings were transplanted at spacing of 15x20 cm in 5.1m2 plot, with one seedling per hill. Date
of flowering, plant height, maturity, grain color, shape, size, pericarp color and aroma were
compared for purification and removal of duplications. Breeding programs were initiated for the
improvement of these national grade aromatic varieties and pure lines (PL) are being evaluated in
multilocation trials.
Key results:
The varieties showed a wide variation in dates of flowering, plant height and grain shape, size,
color and aroma. We isolated and purified 104 accessions and preserved the seeds. PLs were
distinct, for example, Kalijira-PL1 and Kalijira-PL9 were one week earlier and had 0.5 t ha-1 yield
advantage over the original Kalijira check, and their grain morphology is distinguishable from each
other and the original variety. Breeding populations were developed by involving these aromatic
landraces and small grain HYVs.
Synthesis and Applications:
DNA fingerprinting of these varieties is in progress for IPR issue. The pure stocks of seeds are now
ready for sharing with rice scientists and relevant organizations for further improvement. BRAC will
continue to save this heritage through on-farm conservation and proper storage.


IRC14-1296

01d. Taxonomy of rice
TOWARDS A STABLE ORYZA TAXONOMY: BIOSYSTEMATICS RESEARCH IN THE
INTERNATIONAL RICE GENEBANK
M.C.N. Banaticla-Hilario1, M.E.B. Naredo1, M.S.R. Almazan1, S.M.Q. Mercado1, G.L.S. Capilit1,
K.L. McNally1, N.R. Sackville Hamilton1
1
T.T. Chang Genetic Resources Center, International Rice Research Institute, Los Baños,
Philippines
Purpose:
Taxonomic information is vital in documenting and managing plant genetic resources. Accurate
classification and identification of genebank accessions provide a solid foundation for
characterization, evaluation, and utilization of the conserved germplasm. The International Rice
Genebank (IRG) aims to authenticate the taxonomic identity of all the (~4700) wild Oryza
accessions under its custody. Depending on the classification scheme, however, nomenclatural
problems exist in the genus Oryza mainly attributed to (1) presence of diploid and tetraploid forms
in a taxon (2) presence of continuous morphological variation between two taxa.
Approach and methods used:
At the IRG, studies are being conducted to verify relationships between and among taxa based on
various biosystematic evidences such as phenotype-, genotype- and crossability data. Species or
species complex in focus for the problems identified include: 1) the African CC genome species, O.
punctata; 2) the Asian AA genome species O. nivara and O. rufipogon; and 3) species of the O.
meyeriana complex, O. granulata and O. meyeriana.
Key results:
Morphological data on Series Latifoliae species separated the tetraploids from the diploid forms of
O. punctata. This supports the recognition of the tetraploid forms as a distinct species O.
schweinfurthiana. An ecogeographic analysis of O. nivara and O. rufipogon accessions suggested
the treatment of these taxa as separate species based on the following arguments: a) ecological
distinction; b) substantial pre-zygotic isolation; 3) differences in gene flow– and genetic variation
patterns; 4) local scale genetic divergence and 5) reinforced gene flow barriers under sympatric
conditions. Preliminary analyses based on morphological and molecular data support the

treatment of O. granulata and O. meyeriana as distinct species.
Synthesis and Applications:
Through these biosystematic studies, IRG hopes to resolve species relationships and contribute to
a more stable taxonomy for the genus Oryza. The research results can enable the gene bank
community to correctly classify and manage their wild rice collections.


IRC14-0028
01e. Characterization and evaluation of rice genetic diversity, including ‘omics’
GENETIC DIVERSITY AND EXPLORING NOVEL SOURCES OF SALT TOLERANCE IN RICE
THROUGH MOLECULAR CHARACTERIZATION
M.A. Rahman1, M.J. Thomson1, A.M. Ismail2
1
Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute,
Los Baños, Philippines
2
Crop and Environmental Sciences Division, International Rice Research Institute, Los Baños,
Philippines
Purpose:
There is a crucial need to broaden the genetic base for donors of salt tolerance mechanisms for
wider adaptation to stress-prone agro-ecological niches in salt affected areas. The genetic diversity
and characterization of rice across Africa, Bangladesh and the Indian coastal areas is investigated
to identify novel sources of salt tolerance through SSR and SNPs.
Approach and methods used:
The allelic diversity of 107 cultivated rice germplasm has been characterized using molecular
markers (RM1287, AP3206f, RM3412b, RM493 and RM7075) linked to Saltol locus and a highthroughput 384-SNP platform.
Key results:
An overall diversity in SNP markers using Illumina GoldenGate genotyping on a BeadXpress
Reader identified a total of 864 alleles using 384-SNP markers across the 107 rice accessions
ranging from 2.0 alleles per locus, with an average of 13.4% heterozygosity. The polymorphism

information content (PIC) values ranged from 0.02 to 0.58, with an average of 0.35. On average,
65% of the 107 rice accessions shared a common major allele at any given locus. The genetic
distance-based results using UPGMA clustering revealed four distinct groups in this diverse
germplasm. The two japonica varieties, Azucena and Moroberekan, formed a cluster with the
reference variety Nipponbare. The landraces Chinikanai, Noyonmoni, Ranisalute, Gopalbhog,
Jamainadu and Bamonkhir are from Bangladesh and they are popular for their good grain quality,
especially for aroma, and they made a cluster with Basmati370. One cluster was identified as aus
where Agrani, Kasalath, Surjamukhi, Dular, AusBako, Kalisaita and Jaliboro are aus lines of
Bangladeshi origin, and Kalarata and Hasawi are Indian and Saudi Arabia origin, respectively, and
compare with the aus reference line N22 (Nagina22). One cluster was identified as aus with the
tolerant landrace Kalarata falling within that cluster. All of the Pokkali accessions formed a subcluster with in indica group and Pokkali derived tolerant RIL FL478 was located near Pokkali subcluster constituted a sub-group with 93-11. The promising novel donors viz. Akundi, Ashfal,
Capsule, Cheriviruppu, Chikirampatnai, Kalarata and Kutipatnai are genetically different from
Pokkali and Nona Bokra, confirming their potential as novel sources for salinity tolerance.
Synthesis and Applications:
This study shows potential application of high-throughput 384-SNP Illumina GoldenGate
genotyping platform in diversity analysis.


IRC14-0060
01e. Characterization and evaluation of rice genetic diversity, including ‘omics’
CLASSIFICATION OF THE PHOTOPERIOD SENSITIVITY OF PROMISING LINES OF RICE
K. Klakhaeng1, K. Boonsirichai2
1
Rice Department, Ministry of Agriculture and Cooperatives, Bangkok, Thailand
2
-, Thailand Institute of Technology (Public Organization), Nakornnayok, Thailand
Purpose:
This study, which was conducted during 2004-2013, aimed to classify the degree of photoperiod
sensitivity of promising lines of rice at Bureau of Rice Research and Development, Thailand.
Approach and methods used:

Varieties/lines of rice were planted on the first day of April, May and August. They were given ten
hours of day length, 7.00 am - 5.00 pm, in order to obtain the flowering date data. IR58, RD7, Nam
Sa-gui 19, Leuang Pratew 123, Khao Tah Haeng 17, Khao Dawk Mali 105, Sew Mae Jan, Hahng
Yi 71, Niaw Sanpatawng and Pin Gaew 56 were used as the standard varieties for the photoperiod
responsiveness classification. Flowering date data of each variety/line were collected for the
analysis of the basic vegetative phase (BVP), the photoperiod sensitive phase (PSP) and the
degree of sensitivity (Ghose and Saran, 1982; Vergara and Chang, 1985).
Key results:
According to their responses to day length, rice could be classified into 3 groups: essentially
photoperiod insensitive varieties (IR58 and RD7), weakly photoperiod insensitive varieties (Nam
Sa-gui19) and strongly photoperiod sensitive varieties (Khao Dawk Mali105, Niaw Sanpatawng,
Leuang Pratew 123, Sew Mae Jan, Hahng Yi71, Pin Gaew56 and Khao Tah Haeng17).
Measurements of the degree of sensitivity in comparison with the standard varieties served as the
classification criterion. The study was performed on 352 varieties/lines. Of these, 133 were found
essentially photoperiod insensitive, 98 were weakly photoperiod insensitive, while 121 were found
strongly photoperiod sensitive.
Synthesis and Applications:
The degree of sensitivity of the photoperiod insensitive varieties/lines was found to be less than 45
and their BVP varied from short to long. These information will be useful for the recommendation
of appropriate varieties to farmers based on to the day length. Besides, the photoperiod sensitivity
of rice will be useful in rice breeding programs especially essentially photoperiod insensitive
varieties.


IRC14-0224
01e. Characterization and evaluation of rice genetic diversity, including ‘omics’
UNRAVEL POLAR METABOLOME OF THAI JASMINE RICE ASSOCIATED WITH BROWN
PLANTHOPPER INFESTATION USING 1H NMR-BASED METABOLOMICS
U. Uawisetwathana1, S. Graham2, W. Kamolsukyunyong3, W. Sukhaket3, A. Klanchui1,
T. Toojinda3, A. Vanavichit3, N. Karoonuthaisiri1, C. Elliott4

1
Microarray Laboratory, National Center for Genetic Engineering and Biotechnology, Pathumthani,
Thailand
2
Beaumont Health System, Institute of Research, Michigan, USA
3
Rice Gene Discovery Unit,
National Center for Genetic Engineering and Biotechnology Kasetsart University, Nakhon Pathom,
Thailand
4
Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
Purpose:
Up to date, there has never been a study of the brown planthopper (BPH) resistance in Thai rice at
the metabolic level. To improve a selective breeding program of such desirable trait, it is important
to understand the biological mechanism of the response to the BPH. Therefore, polar metabolome
of Thai Jasmine rice (KD) and their BPH resistant isogenic lines was investigated during the BPH
infestation in order to decipher the response mechanism to the infestation and reveal the
intereaction between the plant and insect.
Approach and methods used:
1
H NMR spectroscopy combined with chemometrics were used to analyze the polar metabolome in
leaves extracts of BPH-susceptible KD and their BPH resistant isogenic lines (BPH-resistant IL7
and BPH-resistant+ IL308) before and after BPH infestation at different time points (Days 1, 2, 3, 4
and 8).
Key results:
Physiological responses of the rice isogenic lines were different based on the quantitative trait loci
of BPH resistance. For leaves metabolite profiles, multivariate models could distinguish the profiles
before BPH infestation (control group) from after the infestation (treatment group) at the different
time points; however, the profiles did not show any discrimination among the rice varieties. After
identification and quantification, 16 metabolites were significantly altered by the BPH infestation.

Concentrations of alanine, g-aminobutyrate, glycine, acetate, asparagine and formate were altered
in the early stage (D1-D3) of the infestation whereas concentrations of glucose, sucrose,
guanosine, uridine, uracil, fumarate, succinate, tyrosine, lactate and betaine were altered in the late
stage (D4-D8) of the infestation.
Synthesis and Applications:
The metabolites have caused systematic metabolite alterations involved in nitrogen fixation,
nitrogen assimilation, photosynthesis, photo/dark respiration, TCA cycle and the osmotic regulation
process. This study provides the understanding of metabolic response for Thai Jasmine rice and
their BPH resistant isogenic varieties to BPH infestation. Furthermore, the findings from this study
will help plant scientists narrow down their research for putative pathways explaining the resistant
mechanism of the rice to the BPH in order to find an effective way of preventing and controlling the
damage from the infestation.


IRC14-0281
01e. Characterization and evaluation of rice genetic diversity, including ‘omics’
WHOLE TRANSCRIPTOMIC (RNA) SEQUENCING AND LEAF PHOTOSYNTHETIC RESPONSE
TO SALINITY IN HIGH YIELDING RICE INTROGRESSION LINES DERIVED FROM KMR3 X O.
RUFIPOGON
G. Pushpalatha1, D. Subrahmanyam2, K. Sreenu1, T. Ram2, L.V. Subba Rao2, N. Sarla1,
R.A.I. Vandna3
1
Biotechnology, Directorate of Rice Research, Hyderabad, India
2
Physiology, Directorate of Rice Research, Hyderabad, India
3
Biotechnology, National research centre of plant biotechnology, New Delhi, India
Purpose:
High yielding Backcross Inbred lines (BILs) derived from KMR3 x O. rufipogon (BC2F6-7) were
screened at reproductive stage in pot/soil for salinity tolerance. The most salt tolerant KMR3 IL

K478 and most sensitive K198 were analyzed for whole-transcriptomic studies to identify
differentially expressed genes in response to salt stress
Approach and methods used:
The physiological experiments were conducted with 17 diverse rice genotypes including popular
rice varieties, O. sativa (KMR3) X O. rufipogon (BC2F6-7) introgression lines under two different
concentrations (100 mM and 150 mM) of salt. We studied salinity induced changes in leaf
photosynthetic traits by measuring gas-exchange and chlorophyll fluorescence traits, under
continuously maintained salinity stress conditions at reproductive stage. and the seedlings were
subjected to whole-transcriptomic analysis
Key results:
Salinity treatments (100 and 150 mM NaCl) were imposed at reproductive stage. The data on
fluorescence characteristics indicated that salinity treatments had no significant influence on Fv/Fm
ratio (maximum efficiency of PSII) and yield, indicating that salinity stress did not influence the
primary photochemical efficiency of the leaves. Imposition of salt stress had significantly reduced
photosynthesis rate (Pn), stomatal conductance (gs), transpiration rate (E) and intercellular CO 2
concentration in all the tested genotypes. The reduction in Pn was highest in KMR3 introgression
line K198 where as the reduction was minimum in ILs K458, K463, K-50-13 and K478 indicating
relative tolerance to salinity stress in these ILs. Interestingly, these ILs performed better in terms of
grain yield under moderate salinity treatments than the other popular varieties.
Further, the whole genome transcriptomic analysis was performed to compare differential
expression of genes in the most-tolerant K478 and the most-sensitive K198. The K478 showed 281
up-regulated and 1832 down-regulated genes while S-198 showed 125 up-regulated and 1918
down-regulated genes. Thus, the mechanisms for salt tolerance in selected ILs were derived and
list of differentially expressed genes was identified for salt tolerance
Synthesis and Applications:
The introgressions of KMR3 (O. sativa) with wild rice O.rufipogan has the potential to improve
tolerance and can be used to develop salinity tolerant rice varieties and hybrids. The
transcriptomics analysis resulted in up-regulation of superior transcripts under salt stress
conditions, which can be used for RNAi approaches in response to salinity

IRC14-0289
01e. Characterization and evaluation of rice genetic diversity, including ‘omics’
MULTIPLE LOCI IDENTIFIED IN A GENOME-WIDE ASSOCIATION STUDIES OF INTERNAL
PHOSPHORUS UTILIZATION EFFICIENCY IN RICE
M. Wissuwa1, K. Kondo1, T. Fukuda1, A. Mori1, M.T. Rose2, J. Pariasca-Tanaka1, T. Kretzschmar3,
T.J. Rose4
1
Crop Livestock & Environment Division, JIRCAS, Tsukuba, Japan
2
Centre for Green Chemistry and School of Biological Science, Monash University, Clayton,
Australia
3
Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute (IRRI),
Metro Manila, Philippines
4
Southern Cross Plant Science, Southern Cross University, Lismore, Australia
Purpose:
The realization that phosphorus (P) is a non-renewable, finite and increasingly costly resource has
renewed interest in breeding more P-efficient rice varieties. Internal P efficiency (PUE) is a principal
concern because there has been no progress in breeding for high PUE so far as most resources
have been directed toward enhancing P acquisition. In this study our objective is to assess the
genotypic variation present for PUE within the rice gene pool and to map loci controlling PUE
through Genome-Wide Association Studies (GWAS).
Approach and methods used:
A diverse set of 292 rice accessions were grown in nutrient solutions, assuring each genotype had
access to an equal and low (0.8 mg) amount of P. PUE was then estimated as biomass produced
per P taken up. Associations between PUE data and genotypic variation based on a 44K SNP data
set were mapped using the software TASSEL.
Key results:

Most influential loci for PUE were identified on chromosomes 1, 4, 11, and 12. Highest PUE (2.54 g
biomass mg-1 P) was detected in a group of accessions having a rare haplotype on chromosome
11. This group belonged to the aus subspecies of rice. A second influential and rare haplotype on
chromosome 1 further increased PUE in a group of indica accessions. A unique SNP pattern
surrounded three candidate genes at this locus, possibly suggesting that they were introgressed
from a distant relative and maintained through positive selection in the group of high-PUE
accessions. Expression profiling of genes at this locus identified differential expression patterns for
one candidate gene putatively involved in P redistribution during P deficiency.
Synthesis and Applications:
Efforts to improve the P efficiency of rice presently focus largely on marker assisted introgression
of the Pup1 locus containing the P uptake gene OsPSTOL1. The detection of novel loci enhancing
the efficiency of P utilization for biomass accumulation reported here offers a complementary
approach as promising PUE loci will eventually be combined with Pup1 in a marker assisted
pyramiding approach.


IRC14-0568
01e. Characterization and evaluation of rice genetic diversity, including ‘omics’
MORPHOLOGICAL, MOLECULAR AND QUALITY CHARACTERIZATION OF RICE VARIETIES AND
LANDRACES FROM EASTERN SOURTHEN AFRICA
1
1
2
J. Joachim , P.M. Kusolwa , R. Murori
1
Crop science and production, Sokoine University of Agriculture, Morogoro Urban, Tanzania
2
Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute, Dar Es Salaam,
Tanzania
Purpose:

Morphological and molecular markers are powerful tools in establishing variation among genotypes. The
objective of the study was therefore to determine the morphological, molecular and quality relationships
among cultivated rice varieties and land-races from East and Southern (ESA) region for better decision
making in breeding programs.
Approach and methods used:
1. Assessment of phenotypic diversity using morphological traits
Morphological assessment was done by evaluation of the collected germplasms at Bagamoyo Irrigation
Scheme, Pwani-Tanzania, during wet season in 2013. The experiment was laid out in an Alpha Lattice
Design with three replications. The procedures and descriptors for characterization and evaluation of the
morphological traits of rice was based on the descriptors described by IRRI.
2. Evaluation of the molecular diversity using SSR markers
Genetic variation was determined using a panel of 22 SSR markers derived from the 50 standard SSR
markers from GCP set.
3. Determination of grain quality characteristics
The physical grain quality analysis was carried out at the International Rice Research Institute (IRRI)
research station in Dakawa-Morogoro, Tanzania.

Key results:
Out of 25 morphological traits observed, basal leaf sheath color, leaf blade color, panicle exertion, panicle
type, apiculus color, lemma/palea color, awning, number of days to 50% flowering, days to maturity, leaf
length and width, panicle length, plant height showed most variation among the genotypes.
Among the grain quality traits, milling recovery, degree of milling, 1000 grain weight, brown rice length and
shape showed most variation among the evaluated genotypes. The one hundred and ninety one genotypes
characterized were grouped into seven clusters based on morphology and quality traits.

Synthesis and Applications:
The information on diversity of the characterized genotypes in ESA is expected to assist plant breeders in the
selection of parents for use in the hybridization program. This information will also provide a more rational
basis for expanding the gene pool, eliminating duplicates and for future identification of plant materials that
harbor more valuable alleles for genetic improvement in an effort to increase rice productivity.

IRC14-0599
01e. Characterization and evaluation of rice genetic diversity, including ‘omics’
PERSPECTIVES OF IMPROVING AFRICAN RICE ORYZA GLABERRIMA STEUD IN RICE
BREEDING
Y. agnoun1, M. sie2, K. futakuchi3, R. vodouhe4
1
plant production, faculté des sciences agronomiques, cotonou, Benin
2
genetic diversity and improvement, africarice, cotonou, Benin
3
sustainable productivity and enhancement, africarice, cotonou, Benin
4
west and central africa, bioversity international, cotonou, Benin
Purpose:
O. glaberrima Steud., the African rice species offers hopeful perspectives to develop productive
and resistant interspecific progenies. Traditionally, landraces well-adapted to local conditions have
been good sources for improving the resistance of cultivated rice. In the pass O. glaberrima has
not benefited from intensive breeding activities as it is the case for O. sativa, despite the fact that it
carries numerous important alleles governing useful agronomical traits and resistance against
environmental constraints. Since, it's obvious that the succesful interspecific NERICA varieties
(New Rice for Africa) have significantly contributed to improve farmers' incomes and livelihoods.
But, several investigations and critical reviews revealed some gaps resulting in the non-expression
of O. glaberrima useful genes within NERICA.
Approach and methods used:
Therefore, intra-specific breeding approach is needed to explore and benefit from the useful
genetic diversity of the African rice. The use of this genetic diversity will help to fill gaps previously
observed on interspecific varieties and to develop improved lines, resistant to the multiple
environmental stresses through crossings with O. sativa.

Key results:
In this framework, the recent phenotypic assessment of the wide O. glaberrima collection (about
2,300 accessions) available at Africa Rice Center (AfricaRice) foreshadows a great hope on the
use of this biodiversity to develop new promising lines covering major upland, lowland (rainfed and
irrigated), mangroves and deep water rice ecologies.
Synthesis and Applications:
In this paper, we updated the scientific advances on the African rice with special reference to the
valorisation of its genetic advantages using both conventional and molecular breeding methods as
well as advanced biotechnology to improve local multiples stresses and varieties.


IRC14-0656
01e. Characterization and evaluation of rice genetic diversity, including ‘omics’
IMPROVEMENT OF CAMBODIAN RICE (ORYZA SATIVA L.) USING NEXT-GENERATION
MARKER TECHNOLOGY AND METABOLOMICS
J.C.T. Concepcion1, S. Ouk2, V.D. Daygon1, M. Ouk2, D. Zhao3, M.A. Fitzgerald1
1
School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Australia
2
Plant Breeding Unit, Cambodian Agricultural Research and Development Institute, Phnom Penh,
Cambodia
3
Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute,
Los Banos, Philippines
Purpose:
Grain quality is essentially considered in rice production systems in Cambodian. In a survey
conducted by the ACIAR-funded project of IRRI and the Cambodian Agricultural Research and
Development Institute (CARDI), confirmed that all sectors in the value chain considered Pkha
Rumduol as the best rice variety in Cambodia due to its exceptional sensory and cooking qualities.
This study aims to analyze the metabolites amongst the Cambodian germplasm collection, and

provide rice breeders with the tools to transfer that quality into higher yielding, non-photoperiod
sensitive varieties of rice.
Approach and methods used:
A population of 382 F6 recombinant inbred lines (RILs) derived by single-seed descent from two
Cambodian rice varieties, Phka Rumduol (PRD), an aromatic popular rice variety and the highyielding Thmar Krem (TK) were grown at IRRI’s experimental field during the wet season of 2013
and processed for metabolite profiling at the University of Queensland, Australia. Genetic
characterization of the whole population was carried out using the Infinium 6K SNP genotyping
platform at IRRI. Metabolite profiling for volatile compounds was done on milled rice grains,
absorption of the volatile compounds trapped in the headspace of the glass vial was done using a
SPME Carboxen-PDMS fibre, and separation of volatiles was performed. The GCxGC is coupled
with TOF-MS for identification and quantification of the compounds collected.
Key results:
Discriminatory compounds were detected between PRD and TK and among the recombinant
inbred lines. The main compound of aroma, 2-acetyl-1-pyrroline (2AP), is present in high
concentration in the PRD. Key differences are in the amount of grassy, floral, dairy, fatty, rancid
and faecal notes. PRD has compounds giving floral, popcorn and dairy, whereas TK has a number
of compounds that are associated with unpleasant odours. By mQTL analyses, several QTLs were
found to be associated with the discriminatory compounds.
Synthesis and Applications:
The results of this study provided the first set of genetic and metabolite data to identify the genes
responsible for the quality traits in Cambodian rices and ultimately lead to biomarkers for rice grain
quality targeted for the Cambodian stakeholders.


IRC14-0749
01e. Characterization and evaluation of rice genetic diversity, including ‘omics’
GENETIC DIVERSITY FOR EARLY SEEDLING VIGOUR IN RICE BASED ON MOLECULAR
MARKERS AND PHENOTYPIC DATA
G.V. Rajendra Krishna1, A. Anusha1, C. Manoj1, B. Vishnuvardhan Reddy1, M.S. Ramesha2
1

Biotechnology, Barwale Foundation, Hyderabad, India
2
South Asia Rice Breeding Hub, International Rice Research Institute, Hyderabad, India
Purpose:
Dry direct seeded rice ( DSR ) is a potential resource conserving technology. Availability of efficient
genotypes which respond to good and timely management practices determines the success of
DSR. Rapid germination and emergence and early stage seedling vigour manifested in terms of
better root and shoot growth are some of the important traits needed for DSR. Assessment and
exploitation of genetic diversity for these traits is an important step in breeding for DSR.
Approach and methods used:
Eighteen released varieties and 27 breeding lines of diverse origin were used to assess genetic
diversity for early seedling vigour traits. Phenotypic evaluation of shoot length, root length and
biomass was done using paper towel and slantboard test method. Phenotypic data were analysed
and a dendrogram was constructed using UPGMA.101 genome-wide SSR markers were used to
assess genetic diversity and population structure of accessions which were phenotyped for early
seedling vigour traits
Key results:
Analysis of variance revealed highly significant differences for all the traits. Based on early vigour
traits, 45 genotypes were classified in to two major groups and a sub group. The first group
consisted of high early seedling vigour lines, followed by a sub-group consisting of medium
seedling vigour lines, and the second group consists of low seedling vigour lines. A total of 428
alleles were amplfied using 101 SSR markers. The genetic diversity and polymorphic information
content ranged from 5.47 to 21.35 and 0.04 to 0.81 respectively with regard to genotypic data. All
the primers showed distinct polymorphism among the cultivars studied indicating the robust nature
of microsatellites in revealing polymorphism. A dendrogram was constructed using UPGMA in
respect of genotypic data derived from 101 markers. There were differences in group formation
when the genotypic data was compared with the phenotypic data in relation to trait of interest.
These differences may be due to utilization of randomly selected markers throught out the genome.
Synthesis and Applications:
Utilization of trait specific markers may help in correlating the genotypic data with phenotypic data.

Many promising genotypes with early vigour and good agronomic traits were identified and a few
best donors can be utilized in future breeding programs.


IRC14-0791
01e. Characterization and evaluation of rice genetic diversity, including ‘omics’
DUS TESTS IN RICE AND REGISTRATION OF FARMERS' VARIETIES - INDIAN EXPERIENCE
L.V. Subba Rao1, N. Shobha Rani1, M. Chiranjeevi1, K. Lavanya1, C. Padma1, B. Jayasree1,
U. Chaitanya1, B. Jyothi1, R. Surender1, S.R. Dhua2, S. Rakesh3, P. Borah4, M. Bhaskaran5,
R. Dipal Chowdhury6, B.C. Viraktamath7
1
Plant Breeding, Directorate of Rice Research, Hyderabad, India
2
Plant Breeding, Central Rice Research Institute, Cuttack, India
3
Plant Breeding, IARI, New Delhi, India
4
Plant Breeding, AAU, Jorhat, India
5
Plant Breeding, TNAU, Coimbatore, India
6
DUS, PPV & FRA, New Delhi, India
7
Project Director, Directorate of Rice Research, Hyderabad, India
Purpose:
India being signatory to WTO, it is obligatory to have some sort of protection to the plant varieties
as Indian patent act doesn't recognize patenting life forms. Consequent to this the PPV & FR
Authority was established in 2005, with the objective of providing an effective system of protection
of plant varieties and rights of farmers. Directorate of Rice Research (DRR), Hyderabad has played
a pioneering role in developing the DUS Test guidelines.

Approach and methods used:
DRR as nodal centre conducted the first DUS tests in rice in 2008 with 8 candidate (new) varieties
and since then several new varieties, Farmers' Varieties and Varieties of Common Knowledge
(VCKs) were included in DUS testing. Farmers' varieties are traditionally cultivated and serve as a
reservoir of useful genes. VCKs are plant varieties developed and marketed by the private /public
sector which are not released by the govt. system and yet cultivated by the farmers. Farmers'
varieties, VCKs, any other varieties in public domain and new varieties nominated by different
universities, institutions, companies are tested following the DUS test guidelines of Protection of
Plant varieties and Farmers' Rights Authority (PPV& FRA). The candidate / new varieties are
tested for two seasons at two locations while Farmers Varieties and VCKs are tested for one
season at two locations before granting registration.
Key results:
Registration of extant notified varieties (ENVs) was initiated by the authority along with new
varieties. As on date a total of 24 new varieties, 19 VCKs, 65 Farmers' varieties and 101 ENVs in
rice were registered by PPV & FR authority for which DUS characterization was done at DRR and
other co nodal centres. The DUS test results are submitted to the PPV&FR authority for analysing
the data and granting the Plant Breeders' Rights (PBRs).
Synthesis and Applications:
The question of establishing the Distinctness in Farmers' varieties is a matter of concern.The
Indian law of PPV&FR recognizes the farmers as breeders, conservers, preservers and cultivators
of traditional varieties. Since this great wealth of nation has been conserved by the farmers, simple
characterization of these varieties as per the DUS descriptors, perhaps may be sufficient to grant
the registration.


IRC14-0800
01e. Characterization and evaluation of rice genetic diversity, including ‘omics’
MAINTENANCE OF DATABASE OF REFERENCE COLLECTION VARIETIES (RCVS) VIS-A–
VIS DUS TESTS IN RICE
L.V. Subba Rao1, N. Shobha Rani1, M. Chiranjeevi1, K. Lavanya1, C. Padma1, B. Jayasree1,

U. Chaitanya1, K. Suneetha1, R. Surender1, S.R. Dhua2, S. Rakesh3, P. Borah4, M. Bhaskaran5,
R. Dipal Chowdhury6, B.C. Viraktamath7
1
Plant Breeding, Directorate of Rice Research, Hyderabad, India
2
Plant Breeding, Central Rice Research Institute, Cuttack, India
3
Plant Breeding, IARI, New Delhi, India
4
Plant Breeding, AAU, Jorhat, India
5
Plant Breeding, TNAU, Coimbatore, India
6
DUS, PPV & FRA, New Delhi, India
7
Project Director, Directorate of Rice Research, Hyderabad, India
Purpose:
Reference collections of varieties (RCVs) are maintained to facilitate validation and verification of
distinctness of new varieties under test. In order to establish distinctness, it is necessary to
compare the candidate variety with existing varieties of common knowledge. For this purpose, the
test centers maintain reference collections of authentic samples of seed of existing varieties which
are called as RCVs. The candidate varieties are compared with the appropriate RCVs from the
reference collection in field and laboratory tests for establishing distinctness of test entry.
Approach and methods used:
The experimental material consisted of 543 RCVs which were evaluated in replicated trial for two
seasons during 2012 and 13 at DRR Farm, ICRISAT, Hyderabad. Observations of all the 62 DUS
(Distinctness, Stability, Uniformity) descriptors were recorded on 10 randomly selected plants and
the variability for these descriptors were categorized into different classes and the frequencies of
these traits were determined.
Key results:

Results revealed that among 62 DUS descriptors high diversity was recorded for 35 descriptors
which included essential and additional descriptors. Moderate variation was observed for some of
the descriptors but none of the genotypes have shown variation for the descriptor ‘coleoptile
colour’. With respect to quality traits, the amylose content of these genotypes was found to be
within range of consumer’s preference i.e. intermediate to high. The large genetic diversity present
in this collection for various morphological descriptors will help in DUS Testing in rice for
identification and establishment of distinctness.
Synthesis and Applications:
Therefore maintenance of data base of large number of Reference Collection Varieties is a
prerequisite for the conduct of DUS tests and it occupies pivotal role in this post World Trade
Organization (WTO) era of Intellectual property paving way to Agriculture and Protection of Plant
Varieties.


IRC14-0842
01e. Characterization and evaluation of rice genetic diversity, including ‘omics’
HIGH RESOLUTIONS MELTING ANALYSIS FOR DETECTING OF BADH2 GENE IN THAI RICE
GERMPLASM
K. Soontrajarn1, M. Sanyapeung1, S. Chotechuen1
1
Rice Department, Ministry of Agricultueral and Coperative, Pathumthani, Thailand
Purpose:
Aromatic rice is a specific group of rice having high price in the world rice market. A fragrant trait of
local varieties in the rice germplasm are routinely evaluated by the method of smelling which may
not infer their fragrant genotype.
Approach and methods used:
A recessive gene on chromosome 8 has been elucidated to be homology with the gene encoded
for betaine aldehyde dehydrogenase (BADH2). In fragrant rice this gene was mutated by 8 bp
deletion in exon 7 resulting in accumulation of 2-acetyl-1-pyrroline (2AP). In this study, the
BADEX7-5 primer which is specific for the fragrant gene (badh2) was tested by a conventional

PCR and a Real-time PCR.
Key results:
Both methods showed the same PCR product size of 95 and 103 bp in fragrant and non-fragrant
rice, respectively. High resolutions melting (HRM) analysis demonstrated that the fragrant and
non-fragrant rice were clearly separated by 1 oC difference in Tm. Further experiment could
validate the Real-time PCR condition and components at 10 µl reaction mixture.
Synthesis and Applications:
The method was applied to detect Thai local rice varieties containing “Hom” (Thai word means
fragrant) in their names. The total of 339 tested accessions was found to have two genotypes
including 243 accessions of fragrant rice and 96 accessions of non-fragrant rice. Real-time PCR is
a high-throughput method and can be used to survey fragrant genotype in rice.


IRC14-0856
01e. Characterization and evaluation of rice genetic diversity, including ‘omics’
ALLELE DETERMINATION OF 13 YIELD ENHANCING GENES FROM 367
VARIETIES/LANDRACES USING FLUIDIGM SNP GENOTYPING AND PCR-GEL BASED
METHOD
S.R. Kim1, J. Ramos1, R. Vinarao1, K. Jena1
1
Plant Breeding Genetics and Biotechnology (PBGB) Division,
International Rice Research Institute, Los Baños, Philippines
Purpose:
Rice is the major staple food for more than half of the world’s population. Increasing yield is the
most important target in rice breeding program. Thirteen yield enhancing genes regulating grain
number (Gn1a, LP), panicle branching and grain number (OsSPL14), grain number and culm
strength (SCM2), grain number and heading date (Ghd7), panicle length and grain number (DEP1),
grain size (GW2, GW5, GW8, GS3, GS5, qGL3), and grain weight (TGW6) have been identified.
But the frequency of positive allele for each yield enhancing gene from diverse varieties and
landraces has not been studied.

Approach and methods used:
Here we determined alleles of these genes through detection of putative functional nucleotide
polymorphism (FNP) using Fluidigm SNP genotyping and PCR-gel based method from 367
diversity panel.
Key results:
Most of landraces already had positive alleles for Ghd7 (90.2%), GW8 (88.8%), and SCM2 (85.3%)
genes. GS5 alleles are divided into three alleles (wide, medium, and narrow grain width). Among
them the allele for medium grain width was dominant (55.5%). For Gn1a, we newly identified a new
putative FNPs (3 SNPs) located on the promoter region because 16 bp deletion in the 5’ UTR
region from Gn1a donor (Habataki) was shown in 327 entries (89.1%). Based on new FNPs, 49.0%
has positive allele for grain number. Long grain allele of GS3 and wide grain allele of GW5 were
present in 37.1% and 37.3%, genotypes respectively. Positive alleles for TGW6, DEP1, and SPL14
were very rare (0.003-7.0%). We could not find positive alleles for GW2, qGL3, and LP genes and
Gn1a-null allele from our 367 diversity entries.
Synthesis and Applications:
These results indicate that many varieties lack positive alleles for SPL14, TGW6, DEP1, GW2,
qGL3, and LP genes and these genes can enhance yield potential in many elite varieties by
introducing missing alleles to increase yield potential.


IRC14-0903
01e. Characterization and evaluation of rice genetic diversity, including ‘omics’
THE STUDY OF BADH2 SEQUENCE VARIATION TO UNDERSTAND GENETIC DIVERSITY OF
LANDRACE AND WILD AROMATIC RICE IN THAILAND.
A. Plabpla1, K. Myint2, T. Toojinda1, S. Chotechuen3, C. Vutiyano4, B. Courtois5, A. Vanavichit1
1
Rice Gene Discovery Unit BIOTEC, Kasetsart University, Nakhon-Pathom, Thailand
2
Plant Biotechnology Centre, Ministry of Agriculture and Irrigation, Yangon, Myanmar (Burma)
3

-, Pathum Thani Rice Research Center, Pathum Thani, Thailand
4
-, Rice Department of Thailand, Bangkok, Thailand
5
Cirad, UMR AGAP, Montpellier, France
Purpose:
To study genetic diversity and classification of landrace varieties and wild rice, O. rufipogon, in
Thailand via grain aroma trait.
Approach and methods used:
480 Thai landrace rice varieties were used to study natural variation of grain aroma trait.
Genotyping was performed by five BADH2 gene specific markers included three functional
markers, Aromarker, 3In2AP, and FMbadh2-E2B together with two non-coding markers 5'SSR and
3'Indel. Isozyme group and genome background of 250 selected Thai landrace varieties were
investigated by 19 SSR markers compared to MiniGB dataset and F-AFLP, respectively. 148 and
60 accessions of O. rufipogon and O. nivara, were genotyped by BADH2 functional markers.
Sequence of aromatic wild rice were compared to Thai landrace rice varieties, O. glaberima and
other O. sativa BADH2 sequence from public database.
Key results:
Thai landrace rice varieties, included phase 'Hom' in name, were classified into 27 haplotypes by
five BADH2 specific markers. Genotyping shown 315 out of 480 varieties contained 8 bp deletion
allele, functional marker on exon 7. Isozyme-grouping analysis by SSR markers of landrace
varieties compared with MiniGB dataset suggest almost Thai landrace varieties belong to isozyme
group I. However, aromatic landrace varieties can separated into 5 genome background by
Fluorescent AFLP fingerprinting. Eight bp deletion allele was presented in 4 wild rice accessions
from Phitsanulok, Sukhothai, Trat and Nakorn Ratchasima province. 2AP content of aromatic O.
rufipogon was approximately 0.62 ppm. SNP on BADH2 were detected when compared wild
aromatic rice with O. glaberima and other O. sativa BADH2 sequence from public database.
Synthesis and Applications:
The natural mutant and diversity of landrace and wild aromatic rice in Thailand were explored.
Aromatic landrace rice in Thailand carries the well-known 8-bp deletion on BADH2. However, 165

varieties were not contained 8-bp deletion allele although, they had phase 'Hom' in name. The
recombination event occur in small region BADH2 from 5'SSR, (TA)n on intron 2, and 3'Indel, 43
bp deletion on 3'UTR. Aromatic landrace rice contained 8-bp deletion allele has different genome
background. Variant aromatic landrace varieties can use as a good germplasm source for breeding
program.


IRC14-0906
01e. Characterization and evaluation of rice genetic diversity, including ‘omics’
WHOLE GENOME ANALYSIS OF RICE TERPENE SYNTHASE GENES AND
IDENTIFICATION OF VOLATILE COMPOUNDS INVOLVED IN BROWN PLANTHOPPER
RESISTANCE MECHANISMS IN RICE
W. Kamolsukyunyong1, K. Pitija2, W. Sukhaket3, S. Wongpornchai2, A. Vanavichit1
1
Rice Gene Discovery Unit,
National Center for Genetic Engineering and Biotechnology (BIOTEC) Kasetsart University Kam
phaeng Saen Campus, Nakhon-Pathom, Thailand
2
Department of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science Chiang Mai University, Chiang Mai, Thailand
3
Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon-Pathom,
Thailand
Purpose:
Brown planthopper (BPH) is the most serious insect pest for rice production. Rathu heenati
(RH), the BPH resistance variety, is widely used in breeding program worldwide. Recently,
terpene synthase (TPS) gene of RH was identified to play role in host selection during BPH
infestation however the terpeniod volatile compound products of the gene have not been
identified yet.

Approach and methods used:
To understand the role of TPS in BPH resistance mechanisms of rice at the whole genome
level, genetic variation in rice TPSs were identified by single feature polymorphism (SFP)
mapping, expressions of these TPS genes were analyzed by reverse transcriptase polymerase
chain reaction (RT-PCR) and metabolomic profiling of rice volatile compounds were investigated
by gas chromatography-mass spectrometry (GC-MS) technique.
Key results:
Seventeen TPS genes were identified to contain at least one polymorphic feature between KD
and ILs. Among these genes, two of them, Os04g27430 and Os04g27670, showed differentially
expressed between KD and IL308, on the other hand, four TPS genes did not expressed in both
rice accessions. Eleven volatile compounds, including 7-epi-Susquithujene, Susquithujene, (Z)α-Bergamotene, (E )-α-Bergamotene, (Z)-β-Farnesene , Germacrene D, α-Curcumen, αZingiberene, α-Bisabolene, β-Sesquiphellandrene , and (E )-γ-Bisabolene were found to be
differentially induced in IL308 versus KD after one day of BPH infestation.
Synthesis and Applications:
The present study demonstrates that TPS genes of rice varieties contained polymorphisms that
may affect function of the genes. Moreover, only some rice TPS genes were altered their
expression by BPH infestation. And finally, several volatile compounds were identified as
candidate products of BPH-induced TPS genes. These finding may pave the way for rice pest
management by using rice natural volatile compounds.