Grain yield QTLs with consistent-effect under reproductive-stage drought stress in rice

Bartholome

et al. 2020

Preprint

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Background Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. Results The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. Conclusion These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.

Section: Mas Optimization Based On Signi Cant Genomic Regions Identi Edsupporting

confidence: 67%

Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel

Bhandari

Bartholome

et al. 2020

Preprint

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“…It is important to take note here that the qDTY 1.1 was reported to have significant effect on the grain yield under control non-stress and reproductive stage drought stress in different genetic backgrounds such as Swarna, IR64, MTU1010 under lowland and upland environments (Vikram et al 2011;Sandhu et al 2014;Sandhu et al 2015). The qGY 2-1 and qGY 2-2 reported in the present study were found to be present in the upstream and downstream region of earlier reported qDTY 2.3 , respectively (Sandhu et al 2014;Palanog et al 2014). Interestingly, the qGY 5-2 reported in the present study was located near the earlier reported genes OsRPK1 gene (Chen et al 2013 for root development), OsCCaMK (Bao et al 2014 for microbial symbiosis), OsHAP3B, OsTPS1 (Miyoshi et al 2003 for chloroplast biogenesis), OsSTN8 (Nath et al 2013) for protein phosphorylation of photosystem II) and MTAs for nutrient uptake (Sandhu et al 2019).…”

Section: Mas Optimization Based On Significant Genomic Regions Identisupporting

confidence: 58%

Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel

Bhandari

Bartholome

et al. 2020

Preprint

Self Cite

Background Reproductive-stage drought stress is a major impediment to rice production globally. Conventional and marker-assisted breeding strategies for developing drought tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles and understanding their interactions with genetic backgrounds for contributing to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage drought. A diverse set of 280 indica-aus accessions was phenotyped for grain yield and nine yield-related traits under normal condition and under two managed drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. Results The study identified a total of 220 significant MTAs and candidate gene analysis within 200kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 47 genes, 4 earlier reported major grain yield QTLs and 8 novel QTLs for 10 traits. The significant MTAs were majorly located on chromosomes 1, 2, 5, 6, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related traits, except flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding program targeting grain yield improvement under drought. Conclusion These results provide a promising insight into the complex-genetic architecture of grain yield under reproductive-stage drought under different environments. Validation of major genomic regions reported in the study can be effectively used to develop drought tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.

“…Identification of genetic regions linked to drought tolerance using genotyping strategies such as selective genotyping (SG), whole-genome genotyping (WGG), bulk segregant analysis (BSA) [50,51,167,168], genome-wide association studies (GWAS, an improved version of marker-assisted selection) [169][170][171][172], and successful introgression in different genetic backgrounds using marker-assisted backcrossing [42,46,52,144,167,168,173,174], marker-assisted recurrent selection [175,176], and marker-assisted QTL pyramiding [89] has been reported. Mapping populations segregating for drought-tolerance-related traits led to the identification of 12 quantitative trait loci (QTLs) ( Table 6) showing a large effect against high-yielding, drought-susceptible popular varieties: Swarna, IR64, MTU1010, TDK1, Sabitri, and Vandana [49][50][51][52][53]167,168,[177][178][179][180] (Table 6). Gathering all data on the donors/recipients, factors, traits, genes, mechanisms, and technologies that sustain yield under drought and accumulating them into elite genotypes without negative effects on yield potential could be the best solution for rainfed environments.…”

Section: Marker-assisted Breeding: Identification Introgression Andmentioning

confidence: 99%

Bridging the Rice Yield Gaps under Drought: QTLs, Genes, and their Use in Breeding Programs

Kumar

2017

Agronomy

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Rice is the staple food for more than half of the world's population. Although rice production has doubled in the last 30 years as a result of the development of high-yield, widely adaptable, resource-responsive, semi-dwarf varieties, the threat of a food crisis remains as severe as it was 60 years ago due to the ever-increasing population, water scarcity, labor scarcity, shifting climatic conditions, pest/diseases, loss of productive land to housing, industries, rising sea levels, increasing incidences of drought, flood, urbanization, soil erosion, reduction in soil nutrient status, and environmental issues associated with high-input agriculture. Among these, drought is predicted to be the most severe stress that reduces rice yield. Systematic research on drought over the last 10 years has been conducted across institutes on physiology, breeding, molecular genetics, biotechnology, and cellular and molecular biology. This has provided a better understanding of plant drought mechanisms and has helped scientists to devise better strategies to reduce rice yield losses under drought stress. These include the identification of quantitative trait loci (QTLs) for grain yield under drought as well as many agronomically important traits related to drought tolerance, marker-assisted pyramiding of genetic regions that increase yield under drought, development of efficient techniques for genetic transformation, complete sequencing and annotation of rice genomes, and synteny studies of rice and other cereal genomes. Conventional and marker-assisted breeding rice lines containing useful introgressed genes or loci have been field tested and released as varieties. Still, there is a long way to go towards developing drought-tolerant rice varieties by exploiting existing genetic diversity, identifying superior alleles for drought tolerance, understanding interactions among alleles for drought tolerance and their interaction with genetic backgrounds, and pyramiding the best combination of alleles.