Identification of drought responsive QTLs during vegetative growth stage of rice using a saturated GBS-based SNP linkage map

Bhattarai, Uttam; Subudhi, Prasanta K.

doi:10.1007/s10681-018-2117-3

Cited by 32 publications

(14 citation statements)

References 55 publications

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“…Drought stress increases the days to flowering and reduces the plant height and spikelet fertility resulting in yield loss [4,[11][12][13]. Leaf rolling is an important indicator for measuring drought responsiveness in rice [14,15]. A high average leaf rolling score of US rice germplasm indicated their susceptibility under drought.…”

Section: Discussionmentioning

confidence: 99%

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

Bhattarai

Subudhi

2019

Plants

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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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Section: Discussionmentioning

confidence: 99%

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

Bhattarai

Subudhi

2019

Plants

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“…Molecular markers have been widely used in plant breeding programs. Several different types of markers are available; however, their applications have been restricted in the past due to limitations such as low density, labor intensity, technical requirements, and high cost of large-scale analysis 13 , 14 . The advent of next-generation sequencing (NGS) technologies has resulted in an exponential increase in the number of genetic variants that can be discovered in a single experiment 15 .…”

Section: Introductionmentioning

confidence: 99%

Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm

Delfini

Moda-Cirino

Neto

et al. 2021

Sci Rep

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Brazil is the world's largest producer of common bean. Knowledge of the genetic diversity and relatedness of accessions adapted to Brazilian conditions is of great importance for the conservation of germplasm and for directing breeding programs aimed at the development of new cultivars. In this context, the objective of this study was to analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diversity panel consisting of 219 common bean accessions, most of which belonging to the Mesoamerican gene pool. Genotyping by sequencing (GBS) of these accessions allowed the identification of 49,817 SNPs with minor allele frequency > 0.05. Of these, 17,149 and 12,876 were exclusive to the Mesoamerican and Andean pools, respectively, and 11,805 SNPs could differentiate the two gene pools. Further the separation according to the gene pool, bayesian analysis of the population structure showed a subdivision of the Mesoamerican accessions based on the origin and color of the seed tegument. LD analysis revealed the occurrence of long linkage blocks and low LD decay with physical distance between SNPs (LD half decay in 249 kb, corrected for population structure and relatedness). The GBS technique could effectively characterize the Brazilian common bean germplasms, and the diversity panel used in this study may be of great use in future genome-wide association studies.

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“…GBS is a cost-efficient and effective genotyping method (Yang et al, 2017;Bhattarai & Subudhi, 2018;Hackett et al, 2018). In this study, 390.30 Gb clean reads were generated.…”

Section: Discussion Genetic Purity Genetic Distance and Relationshipsmentioning

confidence: 99%

Development of core-collections for Guizhou tea genetic resources and GWAS of leaf size using SNP developed by genotyping-by-sequencing

Niu

Koiwa

Song

et al. 2020

PeerJ

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An accurate depiction of the genetic relationship, the development of core collection, and genome-wide association analysis (GWAS) are key for the effective exploitation and utilization of genetic resources. Here, genotyping-by-sequencing (GBS) was used to characterize 415 tea accessions mostly collected from the Guizhou region in China. A total of 30,282 high-quality SNPs was used to estimate the genetic relationships, develop core collections, and perform GWAS. We suggest 198 and 148 accessions to represent the core set and mini-core set, which consist of 47% and 37% of the whole collection, respectively, and contain 93-95% of the total SNPs. Furthermore, the frequencies of all alleles and genotypes in the whole set were very well retained in the core set and mini-core set. The 415 accessions were clustered into 14 groups and the core and the mini-core collections contain accessions from each group, species, cultivation status and growth habit. By analyzing the significant SNP markers associated with multiple traits, nine SNPs were found to be significantly associated with four leaf size traits, namely MLL, MLW, MLA and MLSI (P < 1.655E−06). This study characterized the genetic distance and relationship of tea collections, suggested the core collections, and established an efficient GWAS analysis of GBS result. Development of corecollections for Guizhou tea genetic resources and GWAS of leaf size using SNP developed by genotyping-by-sequencing. PeerJ 8:e8572 E, Barreneche T. 2016. Genetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars. BMC Plant Biology 16(1):49 . 2017. Genetic diversity, population structure, and linkage disequilibrium of a core collection of Ziziphus jujuba assessed with genome-wide SNPs developed by genotyping-by-sequencing and SSR markers. L. 2013. Massive sorghum collection genotyped with SSR markers to enhance use of global genetic resources. PLOS ONE 8(4):e59714 DOI 10.1371/journal.pone.0059714. Coan MMD, Senhorinho HJC, Pinto RJB, Scapim CA, Warburton ML. 2018. Genomewide association study of resistance to ear rot by in a tropical field maize and popcorn core collection. Crop Science 58(2):564-578 DOI 10.2135/cropsci2017.05.0322. Cunff LL, Fournier-Level A, Laucou V, Vezzulli S, Lacombe T, Adam-Blondon AF, Boursiquot JM, This P. 2008. Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp. sativa. BMC Plant Biology 8(1):31 Egbadzor KF, Ofori K, Yeboah M, Aboagye LM, Opoku-Agyeman MO, Danquah EY, Offei SK. 2014. Diversity in 113 cowpea [Vigna unguiculata (L) Walp] accessions assessed with 458 SNP markers. Springer Plus 3(1):541

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Identification of drought responsive QTLs during vegetative growth stage of rice using a saturated GBS-based SNP linkage map

Cited by 32 publications

References 55 publications

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

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

Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm

Development of core-collections for Guizhou tea genetic resources and GWAS of leaf size using SNP developed by genotyping-by-sequencing

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