Genome-Wide Association Analysis Reveals the Gene Loci of Yield Traits under Drought Stress at the Rice Reproductive Stage

Abstract

Drought is an important factor limiting the growth and development of rice and thereby seriously affects rice yield. The problem may be effectively solved by dissecting the drought-resistance mechanism of rice, creating excellent drought-resistant germplasm, and mining new drought-resistant genes. In this study, 305 accessions (189 Xian, 104 Geng, 5 Aus, and 7 Basmati) were used to identify drought-related phenotypes such as grain yield per plant (GYP), grain number per panicle (GNP), panicle number per plant (PNP), and plant height (PH) under two-year drought stress. The 2017 GYP and 2018 GNP were Xian max, 2018 GYP, 2017 GNP, 2017 and 2018 PNP, and 2018 PH were Basmati max, and only the 2017 PH was Geng max. The population genetic diversity and population structure were analyzed by combining 404,388 single nucleotide polymorphism (SNP) markers distributed on 12 chromosomes. A total of 42 QTLs with significant correlations was identified, among which 10 were adjacent to the loci reported to be associated with drought resistance. Four candidate genes, LOC_Os03g48890, LOC_Os04g35114, LOC_Os11g45924, and LOC_Os06g38950, were identified by functional annotation and haplotype analysis. The R2 of qGYP3.1 was 11.53%, the R2 of qGNP4.2 was 12.09%, the R2 of qPNP11.1 was 10.01%, and the R2 of qPH6.1 was 13.06%. The results have an important theoretical significance and practical application value for the improvement of drought resistance in rice.

Genome-Wide Association Study of Rice Diversity Panel Reveals New QTLs for Tolerance to Water Deficit Under the Egyptian Conditions

“…For improved adaptability in the dry direct seeded rice (DDSR) system, GWAS conducted by (Subedi et al 2019 ) revealed 37 highly significant MTAs for 20 parameters, including plant and root morphological traits, nutrient uptake, yield, and its components in MAGIC population of 5 different parents. Wang et al ) 2023 (, identified 78 SNPs significantly associated with drought tolerance in the 305 accessions, including 15, 33, 17, and 13 SNPs associated with grain number per plant (GYP), grain number per panicle (GNP), panicle number per plant (PNP), and plant height (PH), respectively. All these 78 significant SNPs were tagged to only 42 QTLs distributed on all 12 chromosomes, which agrees with our finding.…”

“…The agro-climatic conditions have an impact on the cultivation of rice in all the world's rice-growing regions, and crop improvement has historically been considered as a crucial factor in the selection and evolution of improved rice varieties. Soil salinity and water availability for growing rice are two of the most significant agro-climatic conditions that limit yield, even for the advanced rice cultivars (Bhattacharyya et al 2020 ; Wang et al 2023 ; Zampieri et al 2017 ).…”

“…When drought stress occurred during the flowering stage, a spikelet sterility of 73% was noted (Hoang et al 2019 ). While an extensive drought during the grain filling stage decreased grain yield by 75%, one that occurred during the vegetative stage had a minor impact on later plant development, with yield reductions of up to 30% (Bhandari et al 2021 ; Wang et al 2023 ).…”

“…Future genetic advancements in rice productivity will be made possible by adopting an integrative strategy that combines agronomic management techniques with plant breeding, physiological dissection of tolerant traits, and molecular genetic/genomic technology. Alternative to traditional mapping approach, selective genotyping was successfully utilized in rice breeding to map major quantitative trait loci (QTLs) for different traits under stress (Beena et al 2013 , 2018 ; Kimura & Imamoto 2014 ; Mofatto et al 2016 ; Oladosu et al 2019 ; Shakiba et al 2017 ; N. Wang et al 2023 ). Most of these quantitative trait loci (QTLs) have lowered genomic resolution and limited the availability of allelic diversity for positional cloning processes.…”

Toward Food Security in 2050: Gene Pyramiding for Climate-Smart Rice

“…Haplotype-based breeding allows breeders to combine alleles for distinct polymorphisms (such as SNPs, insertions/deletions, and other markers or variants) on the same chromosome that are inherited together with a low possibility of contemporaneous recombina-tion [206]. In this method, specific genomic regions associated with desirable traits related to climate resilience in rice, such as drought tolerance, salt tolerance, heat resistance, disease resistance, and improved yield, are targeted [207][208][209][210].…”