Genome wide association study (GWAS) for grain yield in rice cultivated under water deficit

Abstract

The identification of rice drought tolerant materials is crucial for the development of best performing cultivars for the upland cultivation system. This study aimed to identify markers and candidate genes associated with drought tolerance by Genome Wide Association Study analysis, in order to develop tools for use in rice breeding programs. This analysis was made with 175 upland rice accessions (Oryza sativa), evaluated in experiments with and without water restriction, and 150,325 SNPs. Thirteen SNP markers associated with yield under drought conditions were identified. Through stepwise regression analysis, eight SNP markers were selected and validated in silico, and when tested by PCR, two out of the eight SNP markers were able to identify a group of rice genotypes with higher productivity under drought. These results are encouraging for deriving markers for the routine analysis of marker assisted selection. From the drought experiment, including the genes inherited in linkage blocks, 50 genes were identified, from which 30 were annotated, and 10 were previously related to drought and/or abiotic stress tolerance, such as the transcription factors WRKY and Apetala2, and protein kinases.

Genomic analysis of maize lines introduced in the early stages of a breeding programme

“…In this sense, the marker associated with this region of the genome may be useful for the production of hybrids resistant to water stress. In fact, this notion is the hypothesis of several GWAS for grain yield (Ain et al., ; Ma et al., ; Pantalião et al., ; Sukumaran et al., ; Zhang et al., ). These authors claim the importance of applying GWAS for grain yield and its related traits to incorporate genes tolerant to environmental stress.…”

“…In fact, this notion is the hypothesis of several GWAS for grain yield (Ain et al, 2015;Ma et al, 2016;Pantalião et al, 2016;Sukumaran et al, 2015;Zhang et al, 2017). These authors claim the importance of applying GWAS for grain yield and its related traits to incorporate genes tolerant to environmental stress.…”

“…(), the use of GWAS for yield traits and its components has been limited in maize. In other grasses, such as rice and wheat, this paradigm has been overcome, and several studies have applied GWAS to search for major genes associated with grain yield; for instance, those responsible for tolerance to environmental stress (Ain et al., ; Ma et al., ; Pantalião et al., ; Sukumaran, Dreisigacker, Lopes, Chavez, & Reynolds, ). In the present context, where several lines have arisen from introduced germplasm, that is, temperate sources, a GWAS applied to grain yield may serve as a basis for the discovery of favourable alleles introduced from a tropical background.…”

Marker-Assisted elimination of drought-susceptible accessions in upland rice breeding

“…In upland rice, genetic variation for drought tolerance is available in gene banks (Pantalião et al, 2016), and the useful variability must be better exploited in order to be incorporated into the breeding programs. (Serraj et al, 2011;Kumar et al, 2014).…”

“…Genes related to drought tolerance in rice have recently been obtained via mapping of QTLs (Dixit et al, 2014) and association mapping (Pantalião et al, 2016) by means of single nucleotide polymorphism (SNP) markers, functional genomics, microarrays (Parida et al, 2012;Borah et al, 2017), RNA-Seq (Huang et al, 2014;Silveira et al, 2015) or simply by using candidate genes homologous to those identified in other species (Shaar-Moshe et al, 2015;Abreu et al, 2016). The cost of high-resolution genotyping, as well as sequencing, has fallen year by year, which has opened the possibility of identifying genes related to drought tolerance via wholegenome resequencing (Jain et al, 2014).…”