Using minimum DNA marker loci for accurate population classification in rice (Oryza sativa L.)

Because of the rich diversity among rice accessions grown around the world in distinct environments, traditional methods using morphology, cross compatibility and geography for classifying rice accessions according to different sub-populations have given way to use of molecular markers. Having a few robust markers that can quickly assign population structure to germplasm will facilitate making more informed choices about genetic diversity within seedbanks and breeding genepools. WHICHLOCI is a computer program that selects the best combination of loci for population assignment through empirical analysis of molecular marker data. This program has been used in surveys of plant species, for fish population assignment, and in human ancestry analysis. Using WHICHLOCI, we ranked the discriminatory power of 72 DNA markers used to genotype 1,604 accessions of the USDA rice core collection, and developed panels with a minimum number of markers for population assignment with 99% or higher accuracy. A total of 14 markers with high discriminatory power, genetic diversity, allelic frequency, and polymorphic information content were identified. A panel of just four markers, RM551, RM11, RM224 and RM44, was effective in assigning germplasm accessions to any of five sub-populations with 99.4% accuracy. Panels using only three markers were effective for assignment of rice germplasm to specific sub-populations, tropical japonica, temperate japonica, indica, aus, and aromatic. Assignment to tropical japonica, temperate japonica, or indica sub-populations was highly reliable using 3–4 markers, demonstrated by the high correlation with assignment using 72 markers. However, population assignment to aus and aromatic groups was less reliable, possibly due to the smaller representation of this material in the USDA core collection. More reference cultivars may be needed to improve population assignment to these two groups. This study demonstrated that a small number of DNA markers is effective for classification of germplasm into five sub-populations in rice. This will facilitate rapid screening of large rice germplasm banks for population assignment at a modest cost. The resulting information will be valuable to researchers to verify population classification of germplasm prior to initiating genetic studies, maximizing genetic diversity between sub-populations, or minimizing cross incompatibility while maximizing allelic diversity within specific sub-populations.     

Association mapping for yield and grain quality traits in rice (Oryza sativa L.)

Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits, although only one (RM190) maintained the marker-trait association across years and cultivation. The significant association detected between amylose content and RM190 was in agreement with previous QTL analyses in the literature. Herein, the feasibility of undertaking association analysis in conjunction with germplasm characterization was demonstrated, even when considering low marker density. The high linkage disequilibrium expected in rice lines and cultivars facilitates the detection of marker-trait associations for implementing marker assisted selection, and the mining of alleles related to important traits in germplasm.     

Association mapping of grain color,phenolic content,flavonoid content and antioxidant capacity in dehulled rice

Phytochemicals such as phenolics and flavonoids in rice grain are antioxidants that are associated with reduced risk of developing chronic diseases including cardiovascular disease, type-2 diabetes and some cancers. Understanding the genetic basis of these traits is necessary for the improvement of nutritional quality by breeding. Association mapping based on linkage disequilibrium has emerged as a powerful strategy for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. In this study, genome-wide association mapping using models controlling both population structure (Q) and relative kinship (K) were performed to identify the marker loci/QTLs underlying the naturally occurring variations of grain color and nutritional quality traits in 416 rice germplasm accessions including red and black rice. A total of 41 marker loci were identified for all the traits, and it was confirmed that Ra (i.e., Prp-b for purple pericarp) and Rc (brown pericarp and seed coat) genes were main-effect loci for rice grain color and nutritional quality traits. RM228, RM339, fgr (fragrance gene) and RM316 were important markers associated with most of the traits. Association mapping for the traits of the 361 white or non-pigmented rice accessions (i.e., excluding the red and black rice) revealed a total of 11 markers for four color parameters, and one marker (RM346) for phenolic content. Among them, Wx gene locus was identified for the color parameters of lightness (L*), redness (a*) and hue angle (H ^o). Our study suggested that the markers identified in this study can feasibly be used to improve nutritional quality or health benefit properties of rice by marker-assisted selection if the co-segregations of the marker–trait associations are validated in segregating populations.     

Microsatellite based linkage disequilibrium analyses reveal <Emphasis Type="Italic">Saltol</Emphasis> haplotype fragmentation and identify novel QTLs for seedling stage salinity tolerance in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

A set of 84 diverse rice genotypes were assessed for seedling stage salt tolerance and their genetic diversity using 41 polymorphic SSR markers comprising of 19 Saltol QTL linked and 22 random markers. Phenotypic screening under hydroponics identified three indica landraces (Badami, Shah Pasand and Pechi Badam), two Oryza rufipogon accessions (NKSWR2 and NKSWR17) and one each of Basmati rice (Seond Basmati) and japonica cultivars (Tompha Khau) as salt tolerant, having similar tolerance as of Pokkali and FL478. Among the salt tolerant genotypes, biomass showed positive correlation with shoot fresh weight and negative association with root and shoot Na⁺ content. The results indicated repression of Na⁺ loading within the tolerant plants. Linkage disequilibrium (LD) of the Saltol linked markers was weak, suggestive of high fragmentation of Pokkali haplotype, a result of evolutionary active recombination events. Poor haplotype structure of the Saltol region, may reduce its usefulness in marker assisted breeding programmes, if the target foreground markers chosen are wide apart. LD mapping identified eight robust marker-trait associations (QTLs), of which RM10927 was found linked to root and shoot Na⁺ content and RM10871 with shoot Na⁺/K⁺ ratio. RM271 on chromosome 10, an extra Saltol marker, was found associated to root Na⁺/K⁺ ratio. This marker showed a distinct allele among O. rufipogon accessions. There were also other novel loci detected on chromosomes 2, 5 and 10 influencing salt tolerance in the tested germplasm. Although Saltol remained as the key locus, the role of other genomic regions cannot be neglected in tailoring seedling stage salt tolerance in rice.     

Genetic Diversity and Population Structure in Aromatic and Quality Rice (Oryza sativa L.) Landraces from North-Eastern India

The North-eastern (NE) India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland, Sikkim and Tripura, possess diverse array of locally adapted non-Basmati aromatic germplasm. The germplasm collections from this region could serve as valuable resources in breeding for abiotic stress tolerance, grain yield and cooking/eating quality. To utilize such collections, however, breeders need information about the extent and distribution of genetic diversity present within collections. In this study, we report the result of population genetic analysis of 107 aromatic and quality rice accessions collected from different parts of NE India, as well as classified these accessions in the context of a set of structured global rice cultivars. A total of 322 alleles were amplified by 40 simple sequence repeat (SSR) markers with an average of 8.03 alleles per locus. Average gene diversity was 0.67. Population structure analysis revealed that NE Indian aromatic rice can be subdivided into three genetically distinct population clusters: P1, joha rice accessions from Assam, tai rices from Mizoram and those from Sikkim; P2, chakhao rice germplasm from Manipur; and P3, aromatic rice accessions from Nagaland. Pair-wise F_ST between three groups varied from 0.223 (P1 vs P2) to 0.453 (P2 vs P3). With reference to the global classification of rice cultivars, two major groups (Indica and Japonica) were identified in NE Indian germplasm. The aromatic accessions from Assam, Manipur and Sikkim were assigned to the Indica group, while the accessions from Nagaland exhibited close association with Japonica. The tai accessions of Mizoram along with few chakhao accessions collected from the hill districts of Manipur were identified as admixed. The results highlight the importance of regional genetic studies for understanding diversification of aromatic rice in India. The data also suggest that there is scope for exploiting the genetic diversity of aromatic and quality rice germplasm of NE India for rice improvement.     

Association mapping of yield and its components in rice cultivars

To make advances in rice breeding it is important to understand the relatedness and ancestry of introduced rice accessions, and identify SSR markers associated with agronomically important phenotypic traits, for example yield. Ninety-two rice germplasm accessions recently introduced from seven geographic regions of Africa, Asia, and Latin America, and eleven US cultivars, included as checks, were evaluated for yield and kernel characteristics, and genotyped with 123 SSR markers. The SSR markers were highly polymorphic across all accessions. Population structure analysis identified eight main clusters for the accessions which corresponded to the major geographic regions, indicating agreement between genetic and predefined populations. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping association. LD between linked markers decreased with distance and with a substantial drop in LD decay values between 20 and 30 cM, suggesting it should be possible to achieve resolution down to the 25 cM level. For the 103 cultivars, the complex traits yield, kernel width, kernel length, kernel width/length ratio, and 1000-kernel weight, were estimated by analysis of variety trial data. The mixed linear model method was used to disclose marker-trait associations. Many of the associated markers were located in regions where QTL had previously been identified. In conclusion, association mapping in rice is a viable alternative to QTL mapping based on crosses between different lines.     

Assessment of genetic diversity in Ethiopian cowpea [<Emphasis Type="Italic">Vigna unguiculata</Emphasis> (L.) Walp.] germplasm using simple sequence repeat markers

The genetic diversity of cowpea (Vigna unguiculata L. Walp.) in Ethiopia was analyzed using 19 uniform accessions, 62 variable accessions (yielding 185 sub-types), and two mungbean (Vigna radiata) accessions (four subtypes) as outgroup. A set of 23 polymorphic simple sequence repeat (SSR) markers was identified, and polymorphism in the various accessions was scored by determining amplicon variability. Allele frequency, genetic diversity, and polymorphism information content (PIC) were determined for each SSR marker, and a neighbor joining dendrogram was generated to show the genetic relationship among the individual accessions. A total of 75 allelic variants was defined, with the average number of alleles per locus calculated to be three. The average genetic diversity (D) was 0.47, and PIC was 0.4. Three main clusters were identified by phylogenetic analysis, and the clusters and sub-grouping were supported by STRUCTURE and principal component analysis. This grouping had a moderate fixation index value of 0.075 and gene flow (Nm) of 3.176, indicating that the accessions possess wide diversity within individuals and populations. The accessions showed no clustering by geographical origins. Three well-characterized molecular markers (SSR1, C42-2B, and 61RM2) for race specific resistance to Striga gesnerioides in the cowpea cultivar B301 were used to evaluate the accessions for their potential for use in genetic improvement against this pest. Based on this analysis, only two accessions, 222890–2 from Gambela and 286–2 from the Southern Nations, Nationalities, and Peoples (SNNP) region, were found to cluster with B301 and contain the SSR1 resistance allele. These findings will assist in germplasm conservation efforts by the Institute of Biodiversity and Conservation of Ethiopia, and contribute to future studies aimed at the genetic improvement of local germplasm for improved overall agronomic performance as well as Striga resistance in particular.     

不同国家水稻品种的遗传多样性分析

探讨世界不同国家水稻品种的遗传多样性,旨在为各国品种资源的有效利用提供理论依据。本研究利用63对引物对36份来源于不同国家的水稻品种进行遗传多样性分析。共检测到269个等位基因,每个位点的等位基因数(Na)平均为4.54个,有效等位基因数(Ne)平均为3.22,基因多样性指数(H)平均为0.64,Shannon’s信息指数(I)平均为1.21,引物RM206、RM257、RM410、RM235、RM266的等位基因数较多在7条以上。所处纬度相近的国家或地区的水稻品种之间的遗传距离较近,被聚为同一类群,而所处纬度较远的国家或地区的水稻品种被分到了不同类群。结果表明,水稻品种之间的遗传差异与纬度和地理距离有很大的关系。     

东南亚稻种资源收集与鉴定评价

通过实地考察收集等途径,从东南亚国家引进稻种资源662份,其中野生稻120份,栽培稻542份。对栽培稻资源进行隔离检疫、繁殖以及性状鉴定,获得足够种子并构建引进东南亚栽培稻资源数据库。从栽培稻种质中鉴定发掘出抗褐飞虱材料58份,抗稻瘟病材料9份,抗白叶枯病材料11份,耐盐材料12份。引进的稻种资源拓宽了我国水稻遗传基础,丰富了我国的稻种资源基因库,将在水稻育种及相关研究中发挥积极的作用。     

Association studies of dormancy and cooking quality traits in direct-seeded indica rice

Association analysis was applied to a panel of accessions of Assam rice (indica) using 98 SSR markers for dormancy-related traits and cooking quality. Analysis of population structure revealed 10 subgroups in the population. The mean r ² and D ^′ value for all intrachromosomal loci pairs was 0.24 and 0.51, respectively. Linkage disequilibrium between linked markers decreased with distance. Marker-trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). Genome-wide scanning, detected a total of seven significant marker-trait associations (P < 0.01), with the R ² values ranging from 12.0 to 18.0%. The significant marker associations were for grain dormancy (RM27 on chromosome 2), α-amylase activity (RM27 and RM234 on chromosomes 2 and 7, respectively), germination (RM27 and RM106 on chromosome 2), amylose (RM282 on chromosome 3) and grain length elongation ratio (RM142 on chromosome 4). The present study revealed the association of marker RM27 with traits like dormancy, α-amylase activity and germination. Simple correlation analysis of these traits revealed that these traits were positively correlated with each other and this marker may be useful for simultaneous improvement of these traits. The study indicates the presence of novel QTLs for a few traits under consideration. The study reveals association of traits like dormancy, α-amylase activity, germination, amylose content, grain length elongation ratio with SSR markers indicating the feasibility of undertaking association analysis in conjunction with germplasm characterization.     

湖南同名地方稻资源SSR标记及表现型的比较分析

本研究以湖南种质库中保存的不同来源的同名湖南地方稻种质11组(同近名为1组)共136份为研究材料,进行SSR分子标记及农艺性状比较分析,目的是评价湖南同(近)名地方稻的遗传差异程度,为同(近)名地方稻种质资源的保存、供种以及重点利用种质遴选提供理论依据。研究结果表明,各组同名材料的表型遗传距离数值变化较大,各组最大遗传距离变幅1.25(D6/D13)~1.51(G1/G5),最小遗传距离变幅0.16(E7/E9)~0.81(B2/B11)。各组同名材料的SSR标记相似系数差异也大,最小相似系数变幅0.38~0.71,最大相似系数变幅0.86~1.00;同组内同(近)名材料交叉聚类。基于表型性状遗传距离与基于SSR标记遗传相似系数判别组内材料间遗传关系的结果有一致的,也有存在一定差异的。C8/C11、D16/D18、G1/G2、M2/M3、M2/M6、M3/M6、N2/N4、N5/N6、F2/F25、P3/P4的SSR标记相似系数达0.95以上,而其表现型却有1~3个性状存在有统计学意义的差异,说明供试同名材料有明显变异,即使同(近)名但也都值得保存。同时也证实了24对SSR标记分析同名地方稻遗传多样性的不足。     

Transferability of microsatellite and sequence tagged site markers in Oryza species

The genus Oryza comprises 22 species which are potentially useful as a source of genetic variability that can be introgressed into the worldwide cultivated rice, Oryza sativa. Molecular markers are useful tools for monitoring gene introgressions and for detecting polymorphism among species. In this study, cross-amplification was estimated among 28 accessions of 16 Oryza species, representing the genomes AA, BB, CC, BBCC and CCDD, using 59 microsatellite (OG, OS and RM series) and 15 STS (Sequence Tagged Sites) markers. All markers amplified at least one Oryza species, indicating different levels of transferability across species. Markers based on microsatellite sequences amplified 37 % of the accessions, with an average of 6.58 alleles per locus and an average polymorphism information content (PIC) of 70 %. For STS markers, the amplification level was 53.3 %, and the average number of alleles and PIC values were 1.6 and 10 %, respectively. These Results showed that although the STS markers detected a reduced level of genetic diversity, the transferability was higher, indicating that they can be used for genetic analysis when evaluating less genetically related species of Oryza. Among the microsatellite markers, an analysis of species with an AA genome showed that the OG markers produced the highest level of polymorphic loci (54.6 %), followed by RM markers (48 %). Highly polymorphic and transferable molecular markers in Oryza can be useful for exploiting the genetic resources of this genus, for detecting allelic variants in loci associated with important agronomic traits, and for monitoring alleles introgressed from wild relatives to cultivated rice.     

Mapping QTLs for improving grain yield using the USDA rice mini-core collection

Yield is the most important and complex trait for genetic improvement in crops, and marker-assisted selection enhances the improvement efficiency. The USDA rice mini-core collection derived from over 18,000 accessions of global origins is an ideal panel for association mapping. We phenotyped 203 O. sativa accessions for 14 agronomic traits and identified 5 that were highly and significantly correlated with grain yield per plant: plant height, plant weight, tillers, panicle length, and kernels/branch. Genotyping with 155 genome-wide molecular markers demonstrated 5 main cluster groups. Linkage disequilibrium (LD) decayed at least 20 cM and marker pairs with significant LD ranged from 4.64 to 6.06% in four main groups. Model comparisons revealed that different dimensions of principal component analysis affected yield and its correlated traits for mapping accuracy, and kinship did not improve the mapping in this collection. Thirty marker–trait associations were highly significant, 4 for yield, 3 for plant height, 6 for plant weight, 9 for tillers, 5 for panicle length and 3 for kernels/branch. Twenty-one markers contributed to the 30 associations, because 8 markers were co-associated with 2 or more traits. Allelic analysis of OSR13, RM471 and RM7003 for their co-associations with yield traits demonstrated that allele 126 bp of RM471 and 108 bp of RM7003 should receive greater attention, because they had the greatest positive effect on yield traits. Tagging the QTLs responsible for multiple yield traits may simultaneously help dissect the complex yield traits and elevate the efficiency to improve grain yield using marker-assisted selection in rice.     

Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection

A rice mini-core collection consisting of 217 accessions has been developed to represent the USDA core and whole collections that include 1,794 and 18,709 accessions, respectively. To improve the efficiency of mining valuable genes and broadening the genetic diversity in breeding, genetic structure and diversity were analyzed using both genotypic (128 molecular markers) and phenotypic (14 numerical traits) data. This mini-core had 13.5 alleles per locus, which is the most among the reported germplasm collections of rice. Similarly, polymorphic information content (PIC) value was 0.71 in the mini-core which is the highest with one exception. The high genetic diversity in the mini-core suggests there is a good possibility of mining genes of interest and selecting parents which will improve food production and quality. A model-based clustering analysis resulted in lowland rice including three groups, aus (39 accessions), indica (71) and their admixtures (5), upland rice including temperate japonica (32), tropical japonica (40), aromatic (6) and their admixtures (12) and wild rice (12) including glaberrima and four other species of Oryza. Group differentiation was analyzed using both genotypic distance Fst from 128 molecular markers and phenotypic (Mahalanobis) distance D(2) from 14 traits. Both dendrograms built by Fst and D(2) reached similar-differentiative relationship among these genetic groups, and the correlation coefficient showed high value 0.85 between Fst matrix and D(2) matrix. The information of genetic and phenotypic differentiation could be helpful for the association mapping of genes of interest. Analysis of genotypic and phenotypic diversity based on genetic structure would facilitate parent selection for broadening genetic base of modern rice cultivars via breeding effort.     

Potential of SNP markers for the characterization of Brazilian cassava germplasm

Key message

High-throughput markers, such as SNPs, along with different methodologies were used to evaluate the applicability of the Bayesian approach and the multivariate analysis in structuring the genetic diversity in cassavas.

Abstract

The objective of the present work was to evaluate the diversity and genetic structure of the largest cassava germplasm bank in Brazil. Complementary methodological approaches such as discriminant analysis of principal components (DAPC), Bayesian analysis and molecular analysis of variance (AMOVA) were used to understand the structure and diversity of 1,280 accessions genotyped using 402 single nucleotide polymorphism markers. The genetic diversity (0.327) and the average observed heterozygosity (0.322) were high considering the bi-allelic markers. In terms of population, the presence of a complex genetic structure was observed indicating the formation of 30 clusters by DAPC and 34 clusters by Bayesian analysis. Both methodologies presented difficulties and controversies in terms of the allocation of some accessions to specific clusters. However, the clusters suggested by the DAPC analysis seemed to be more consistent for presenting higher probability of allocation of the accessions within the clusters. Prior information related to breeding patterns and geographic origins of the accessions were not sufficient for providing clear differentiation between the clusters according to the AMOVA analysis. In contrast, the F _ST was maximized when considering the clusters suggested by the Bayesian and DAPC analyses. The high frequency of germplasm exchange between producers and the subsequent alteration of the name of the same material may be one of the causes of the low association between genetic diversity and geographic origin. The results of this study may benefit cassava germplasm conservation programs, and contribute to the maximization of genetic gains in breeding programs.     

Genetic diversity and population structure of pummelo (<Emphasis Type="Italic">Citrus maxima</Emphasis>) germplasm in China

Pummelo (Citrus maxima) is one of the basic species of Citrus. It has been cultivated for about 4000 years in China, and therefore, there are abundant germplasm during the long time of culture. However, there is still a lack of a detailed study of the genetic characteristics of pummelo population. In this study, genetic diversity and population structure among 274 pummelo accessions collected in China were analyzed using 31 nuclear simple sequence repeat (nSSR) markers. The observed heterozygosity was calculated as 0.325 and genetic differentiation Fst as 0.077. Genetic structure analysis divided the whole germplasm into three subpopulations, Pop-a, Pop-b, and Pop-c. Pop-a was composed of accessions mostly from Southeast China, Pop-b was composed of accessions from the central region of South China, and Pop-c was composed of accessions from Southwest China. Meanwhile, the analysis of principal coordinate analysis and neighbor-join tree supported the viewpoint of three subpopulations, and then the possible dispersal routes of pummelos in China were proposed. This study provides an insight into the genetic diversity, facilitates future genome-wide association studies, and promotes the breeding program of pummelo as well.     

中国稻种资源收集、保存和更新现状

截止2003年,我国共编目稻种资源77541份,其中各种类型所占百分比大小顺序为:地方稻种(68.68%)、国外引进稻种(12.65%)、野生稻种(9.45%)、选育稻种(6.96%)、杂交稻"三系"资源(2.09%)、遗传标记材料(0.16%);在国家长期库中共保存稻种资源69133份,其中各种类型所占百分比大小顺序为:地方稻种(71.38%)、国外引进稻种(12.16%)、野生稻种(8.09%)、选育稻种(6.52%)、杂交稻"三系"资源(1.54%)、遗传标记材料(0.18%)、其他(0.12%).加强选育品种、品系、突变体的收集和保存;重视国外稻种资源的收集与引进;开展地方稻种的纯系筛选与保存;持续开展稻种资源的繁种更新;开展已筛选优异种质资源的确认和提供利用,这是今后稻种资源收集和保存工作的重要研究任务.     

Assessment of genetic diversity in Italian rice germplasm related to agronomic traits and blast resistance (<Emphasis Type="Italic">Magnaporthe</Emphasis><Emphasis Type="Italic">oryzae</Emphasis>)

Italy is the only country in Europe with a significant land area used for rice production. In this paper, the genetic diversity of 172 national varieties and 47 foreign accessions (ITALORYZA collection) was investigated using a set of neutral markers evenly distributed throughout the 12 chromosomes. Out of the 218 alleles detected in our analysis, 17 and 29% were specific to the Italian and foreign accessions, respectively. From the neighbour-joining tree generated, six sub-groups of temperate japonica germplasm were identified. Plant height and grain type measured in the source collection were fitted to the phylogenetic tree, along with the period of variety registration. This integrated genotype–phenotype analysis revealed that specific sub-groups are characterized by uniform classes of grain type, or by similar plant size, or by period of release in the market. The whole collection was also evaluated for leaf blast resistance by inoculating the plants with three strains of Magnaporthe oryzae, representing the pathogen genetic diversity existing in Italy. Only 15 out of 172 Italian accessions (8.7%) were resistant to all three fungal strains. The correlation between genotype and leaf blast phenotype revealed that the most highly resistant Italian varieties are included in a single germplasm sub-group derived from US varieties. This study represents the starting point for carrying out detailed phenotype–genotype whole-genome association studies and identification of the genetic basis of important agronomic traits for rice cultivation in temperate climates.     

Genetic Variation and Association Analysis of the SSR Markers Linked to the Major Drought-Yield QTLs of Rice

Drought is one of the major abiotic stresses, which hampers the production of rice worldwide. Informative molecular markers are valuable tools for improving the drought tolerance in various varieties of rice. The present study was conducted to evaluate the informative simple sequence repeat (SSR) markers in a diverse set of rice genotypes. The genetic diversity analyses of the 83 studied rice genotypes were performed using 34 SSR markers closely linked to the major quantitative trait loci (QTLs) of grain yield under drought stress (qDTYs). In general, our results indicated high levels of polymorphism. In addition, we screened these rice genotypes at the reproductive stage under both drought stress and nonstressful conditions. The results of the regression analysis demonstrated a significant relationship between 11 SSR marker alleles and the plant paddy weight under stressful conditions. Under the nonstressful conditions, 16 SSR marker alleles showed a significant correlation with the plant paddy weight. Finally, four markers (RM279, RM231, RM166, and RM231) demonstrated a significant association with the plant paddy weight under both stressful and nonstressful conditions. These informative-associated alleles may be useful for improving the crop yield under both drought stress and nonstressful conditions in breeding programs.