Genetic Diversity, Population Structure, and Marker-Trait Association for Drought Tolerance in US Rice Germplasm

Drought is a major constraint in some rice-growing areas of the United States. Its impact is most severe at the reproductive stage resulting in low grain yield. Therefore, assessment of genetic and phenotypic variation for drought tolerance in US rice germplasm is necessary to accelerate the breeding effort. Evaluation of 205 US rice genotypes for drought tolerance at the reproductive stage revealed tolerant response in rice genotypes Bengal, Jupiter, Cypress, Jazzman, Caffey, and Trenasse. Harvest index and fresh shoot weight were identified as important traits to explain the majority of variability among the genotypes under drought tolerance. Genotyping with 80 SSR markers indicated a low level of genetic diversity in US germplasm. Population structure analysis grouped the genotypes into eight clusters. The genotypes from California, Louisiana, and Arkansas formed distinct subgroups. Texas genotypes were similar to those from Louisiana and Arkansas. Marker-trait association analysis showed significant association of RM570 and RM351 with grain yield, spikelet fertility, and harvest index whereas shoot dry weight showed association with RM302 and RM461. The drought-tolerant genotypes identified in this study and the SSR markers associated with drought tolerance attributes will be helpful for development of improved drought-tolerant rice varieties through marker assisted selection.

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Genetic Diversity of Selected Rice Genotypes under Water Stress Conditions

Plants ◽

10.3390/plants10010027 ◽

2020 ◽

Vol 10 (1) ◽

pp. 27

Author(s):

Mahmoud M. Gaballah ◽

Azza M. Metwally ◽

Milan Skalicky ◽

Mohamed M. Hassan ◽

Marian Brestic ◽

...

Keyword(s):

Genetic Diversity ◽

Water Stress ◽

Drought Stress ◽

Drought Tolerance ◽

Ssr Markers ◽

Similarity Index ◽

Stress Conditions ◽

Yield Potential ◽

Drought Tolerant ◽

Rice Genotypes

Drought is the most challenging abiotic stress for rice production in the world. Thus, developing new rice genotype tolerance to water scarcity is one of the best strategies to achieve and maximize high yield potential with water savings. The study aims to characterize 16 rice genotypes for grain and agronomic parameters under normal and drought stress conditions, and genetic differentiation, by determining specific DNA markers related to drought tolerance using Simple Sequence Repeats (SSR) markers and grouping cultivars, establishing their genetic relationship for different traits. The experiment was conducted under irrigated (normal) and water stress conditions. Mean squares due to genotype × environment interactions were highly significant for major traits. For the number of panicles/plants, the genotypes Giza179, IET1444, Hybrid1, and Hybrid2 showed the maximum mean values. The required sterility percentage values were produced by genotypes IET1444, Giza178, Hybrid2, and Giza179, while, Sakha101, Giza179, Hybrid1, and Hybrid2 achieved the highest values of grain yield/plant. The genotypes Giza178, Giza179, Hybrid1, and Hybrid2, produced maximum values for water use efficiency. The effective number of alleles per locus ranged from 1.20 alleles to 3.0 alleles with an average of 1.28 alleles, and the He values for all SSR markers used varied from 0.94 to 1.00 with an average of 0.98. The polymorphic information content (PIC) values for the SSR were varied from 0.83 to 0.99, with an average of 0.95 along with a highly significant correlation between PIC values and the number of amplified alleles detected per locus. The highest similarity coefficient between Giza181 and Giza182 (Indica type) was observed and are susceptible to drought stress. High similarity percentage between the genotypes (japonica type; Sakha104 with Sakha102 and Sakha106 (0.45), Sakha101 with Sakha102 and Sakha106 (0.40), Sakha105 with Hybrid1 (0.40), Hybrid1 with Giza178 (0.40) and GZ1368-S-5-4 with Giza181 (0.40)) was also observed, which are also susceptible to drought stress. All genotypes are grouped into two major clusters in the dendrogram at 66% similarity based on Jaccard’s similarity index. The first cluster (A) was divided into two minor groups A1 and A2, in which A1 had two groups A1-1 and A1-2, containing drought-tolerant genotypes like IET1444, GZ1386-S-5-4 and Hybrid1. On the other hand, the A1-2 cluster divided into A1-2-1 containing Hybrid2 genotype and A1-2-2 containing Giza179 and Giza178 at coefficient 0.91, showing moderate tolerance to drought stress. The genotypes GZ1368-S-5-4, IET1444, Giza 178, and Giza179, could be included as appropriate materials for developing a drought-tolerant variety breeding program. Genetic diversity to grow new rice cultivars that combine drought tolerance with high grain yields is essential to maintaining food security.

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Utilize of genetic diversity and marker-trait association to improve drought tolerance in rice (Oryza sativa L.)

10.21203/rs.3.rs-29383/v1 ◽

2020 ◽

Author(s):

Mohamed I. Ghazy ◽

Khaled. F. Salem ◽

Ahmed Sallam

Keyword(s):

Genetic Diversity ◽

Drought Tolerance ◽

Grain Yield ◽

Oryza Sativa L ◽

Phenotypic Correlation ◽

Phenotypic Traits ◽

Yield Traits ◽

Drought Tolerant ◽

Drought Conditions ◽

Rice Genotypes

Abstract Drought stress in one of the main problems for rice crop as it reduces the production and productivity of the grain yield significantly. In Egypt, many restrictions were made on the cultivation of rice due to its high water demand. Producing promising drought-tolerant rice cultivars in a combination with high yielding is one of the main targets for rice breeders. To address this challenge, a set of 22 highly diverse rice genotypes were evaluated under normal and drought conditions. Morphological, physiological, yield traits were recorded on each genotype. Drought susceptibility index (DSI) was estimated for six yield traits to identify the most drought-tolerant rice genotypes. High genetic variation was found among genotypes tested in the experiment. Under normal conditions, the highest phenotypic correlation was found between grain yield (GY) and sterility percentage (SP) (- 0.73**), while, it was among GY and chlorophyll content (CC) (0.82**) under drought conditions. To identify quantitative trait loci (QTL) controlling yielding traits under drought and normal, single marker analysis was performed between all yield traits under both condition and a set of 106 simple sequence repeat (SSR) marker alleles. The genetic association analysis revealed 14 and 17 QTL under drought and normal conditions, respectively. The most drought-tolerant genotypes were selected based on DSI, the number of QTL in each selected genotypes, and the level of genetic diversity. As a result, five genotypes (Giza 178, IET1444, GZ1368-S-5-4, Nahda, Giza 14) were identified as the most promising drought-tolerant rice genotypes. Eight QTL controlling drought tolerance were identified in Giza 178, Nahda, and GZ1368-S-5-4, while, four QTL were found in IET1444. The number of different QTLs were estimated among the five selected genotypes. Giza 178 and GZ1368-S-5-4 shared the same QTLs. Seven different QTLs were found among Nahda, IET1444, GZ1368-S-5-4, and Giza 14. Combining information from phenotypic traits, genetic diversity analysis, and QTL identification was very useful in identifying the true drought-tolerant rice genotypes that can be used for crossing in the future breeding program.

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Assessment of the genetic diversity and population structure of rice genotypes using SSR markers

Acta Agriculturae Scandinavica Section B - Soil & Plant Science ◽

10.1080/09064710.2019.1670859 ◽

2019 ◽

Vol 70 (1) ◽

pp. 76-86 ◽

Cited By ~ 3

Author(s):

William Titus Suvi ◽

Hussein Shimelis ◽

Mark Laing ◽

Isack Mathew ◽

Admire Isaac Tichafa Shayanowako

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Rice Genotypes

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Validation of Drought Tolerance Gene-linked Microsatellite Markers and Their Efficiency for Diversity Assessment in a Set of Soybean Genotypes

Current Journal of Applied Science and Technology ◽

10.9734/cjast/2021/v40i2531515 ◽

2021 ◽

pp. 48-57

Author(s):

Nishi Mishra ◽

M. K. Tripathi ◽

Niraj Tripathi ◽

Sushma Tiwari ◽

Neha Gupta ◽

...

Keyword(s):

Genetic Diversity ◽

Drought Tolerance ◽

Ssr Markers ◽

Diversity Analysis ◽

Molecular Screening ◽

Genetic Diversity Analysis ◽

Drought Tolerant ◽

Diversity Assessment ◽

Soybean Genotypes ◽

Tolerance Gene

Aim: Soybean is well-thought-out to be a major crop owing to its significant involvement as vegetable oil and protein in human diet. However, inopportunely, its production has been melodramatically declined attributable to the commonness of drought related stress. Study Design: During the present study a total of 53 soybean genotypes were selected. For molecular diversity analysis as well as validation total 12 SSR markers were used. Molecular screening of soybean genotypes was done to determine the efficiency of available markers in genetic diversity analysis as well as their validation on the basis of their association with drought tolerance gene. Place and Duration of the Study: The present study was conducted at Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Gwalior, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, M.P., India during the year 2018 - 2019. Methodology: Template DNA of all 53 selected soybean genotypes extracted for molecular screening. The current investigation has been accomplished to validate the available SSR markers with their efficiency in genetic diversity analysis in a set of soybean genotypes. Results: Among applied drought tolerance gene-linked 12 SSR molecular markers, the highest genetic diversity (0.6629) was noticed in Satt520 while lowest (0.0370) was in Satt557 with an average of 0. 3746.While, the highest PIC value was 0.5887 prearranged by Satt520 and lowest 0.0363 by Satt557 with the mean worth of 0.3063. Conclusion: Dendrogram constructed on the basis of banding profile of employed markers was able to discriminate some putative drought tolerant genotypes i.e., JS97-52, JS95-60 from rest of the genotypes. The results of the present examination may donate towards enhancement of soybean genotypes to bread drought tolerant varieties.

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Early Maturing Drought Tolerant Rice Variety BRRI dhan71 Suitable for Drought Prone Environment in Bangladesh

International Journal of Plant & Soil Science ◽

10.9734/ijpss/2020/v32i1230347 ◽

2020 ◽

pp. 1-11

Author(s):

Md. Abdul Kader ◽

Tamal Lata Aditya ◽

Ratna Rani Majumder ◽

Tapas Kumer Hore ◽

Md. Ehsanul Haq

Keyword(s):

Drought Tolerance ◽

Grain Yield ◽

Amylose Content ◽

Rice Variety ◽

Standard Condition ◽

Reproductive Stage ◽

Severe Drought ◽

Drought Condition ◽

Drought Tolerant ◽

Early Maturing

Drought is the second most treacherous climate-related risk for rice production in rainfed lowland areas. To counter this climate vulnerability, a new rice variety with enhanced drought tolerance was developed. The promising line IR82589-B-B-84-3 was subjected to advanced yield trials to evaluate specific and general adaptability with standard check in on-station as well as on-farm conditions of Bangladesh following randomized complete block (RCB) design with three replications in wet (T. Aman) season. IR82589-B-B-84-3 was developed as a drought-tolerant rice variety BRRI dhan71, which plant height 108 cm and growth duration 115 days after proper evaluation by National Seed Board (NSB) Bangladesh. It was found that this variety is the higher drought tolerance (up to 28 days) during reproductive stage. It can produce 5.5 t/ha grain yield in standard condition and 4.0 t/ha grain yield in medium drought condition but 3.0-3.5 t/ha grain yield in severe drought condition. Grain yield is also not affected by water scarcity during reproductive stage where parch water table depth is more than 70-80 cm from the surface and reduced soil moisture (<20%). Thousand grain weight of the variety is 24 gm, amylose content is 24%. It has long, erect and deep green colored flag leaf. The results indicated that farmers can maximize net profit by cultivating BRRI dhan71 because it required less input, early maturing than existing varieties, drought tolerant and they also get opportunity to cultivate Mustard, Barley, Potato and vegetables after harvesting it. Thus total productivity will be augmented and food security can also be sustained by the cultivation of BRRI dhan71.

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Variability Assessment for Root and Drought Tolerance Traits and Genetic Diversity Analysis of Rice Germplasm using SSR Markers

Scientific Reports ◽

10.1038/s41598-019-52884-1 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 7

Author(s):

H. Verma ◽

J. L. Borah ◽

R. N. Sarma

Keyword(s):

Population Structure ◽

Drought Tolerance ◽

Ssr Markers ◽

Diversity Analysis ◽

Rice Accession ◽

North East India ◽

North East ◽

Population Structure Analysis ◽

Rice Genotypes ◽

Shoot Weight

Abstract The studies on genetic variation, diversity and population structure of rice germplasm of North East India could be an important step for improvements of abiotic and biotic stress tolerance in rice. Genetic diversity and genetic relatedness among 114 rice genotypes of North East India were assessed using genotypic data of 65 SSR markers and phenotypic data. The phenotypic diversity analysis showed the considerable variation across genotypes for root, shoot and drought tolerance traits. The principal component analysis (PCA) revealed the fresh shoot weight, root volume, dry shoot weight, fresh root weight and drought score as a major contributor to diversity. Genotyping of 114 rice genotypes using 65 SSR markers detected 147 alleles with the average polymorphic information content (PIC) value of 0.51. Population structure analysis using the Bayesian clustering model approach, distance-based neighbor-joining cluster and principal coordinate analysis using genotypic data grouped the accession into three sub-populations. Population structure analysis revealed that rice accession was moderately structured based on FST value estimates. Analysis of molecular variance (AMOVA) and pairwise FST values showed significant differentiation among all the pairs of sub-population ranging from 0.152 to 0.222 suggesting that all the three subpopulations were significantly different from each other. AMOVA revealed that most of the variation in rice accession mainly occurred among individuals. The present study suggests that diverse germplasm of NE India could be used for the improvement of root and drought tolerance in rice breeding programmes.

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Study on genetic diversity and population structure of upland rice accessions using SSR markers associated with grain yield under drought

Crop Research ◽

10.5958/2454-1761.2017.00015.8 ◽

2017 ◽

Vol 52 (4and5) ◽

pp. 180

Author(s):

Rahul K. Verma ◽

S. K. Chetia ◽

Anjum Rahman ◽

P. C. Dey ◽

P. Sen ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Grain Yield ◽

Ssr Markers ◽

Upland Rice

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Genetic Diversity Among Some Rice Genotypes with Different Drought Tolerance based on SSR Markers

Cercetari Agronomice in Moldova ◽

10.1515/cerce-2016-0024 ◽

2016 ◽

Vol 49 (3) ◽

pp. 39-50 ◽

Cited By ~ 3

Author(s):

H.A. Freeg ◽

G.B. Anis ◽

A.A. Abo-Shousha ◽

A.N. El-Banna ◽

A. El-Sabagh

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Drought Tolerance ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Allelic Diversity ◽

Similarity Coefficients ◽

Wide Range ◽

Single Marker ◽

Rice Genotypes

Abstract Rice is the most important food crop for the developing world. Hence, identifying rice genotypes to drought tolerance for using as donors in breeding is one of the most important challenges for rice research. Therefore, Molecular markers are useful tools to determine genetic diversity and identifying rice genotypes to drought tolerance. In the present study, A number of 41 rice genotypes with different drought tolerance from different geographic locations were evaluated for genetic diversity by using 15 SSR markers. A total of 68 alleles were detected of which 61(89.79%) were polymorphic. The number of alleles detected by a single marker varied from 2 to 8 alleles with an average of 4.71 alleles per locus. The polymorphic information content (PIC) values ranged from 0.07 (RM219) to 0.80 (RM263) with an average of 0.52. Genetic similarity coefficients of pair wise comparisons were estimated on the basis of the polymorphic microsatelite loci ranged from 0.23 to 0.91 indicating a wide range of genetic variation present among the studied genotypes. It was determined that the primers RM20A, RM302, RM212 and RM286 could be useful for selecting drought tolerant lines through MAS approach. The most significant application of these identified major QTLs for drought tolerance is to collect those favorable alleles into elite local line through marker assisted breeding. The results indicated the ability of SSR markers to identify the allelic diversity and genetic variation among the studied rice genotypes. These results recommended for using this material in future breeding programs to provide important source of genetic diversity for drought tolerance in rice.

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