Mining Beneficial Genes for Aluminum Tolerance Within a Core Collection of Rice Landraces Through Genome-Wide Association Mapping With High Density SNPs From Specific-Locus Amplified Fragment Sequencing

Abstract

Trivalent Aluminum (Al3+) in acidic soils is harmful to root growth and significantly reduce crop yields. Therefore, mining beneficial genes for Al tolerance is valuable for rice production. The objective of this research is to identify some beneficial genes for Al tolerance from rice landraces with high density SNP set from SLAF-seq (Specific-Locus Amplified Fragment sequencing). A total of 67,511 SNPs were obtained from SLAF-seq and used for genome-wide association study (GWAS) for Al tolerance with the 150 accessions of rice landraces in the Ting's rice core collection. The results showed that rice landraces in the Ting's rice core collection possessed a wide-range of variation for Al tolerance, measured by relative root elongation (RRE). With the mixed linear models, GWAS identified a total of 25 associations between SNPs and Al tolerant trait with p < 0.001 and false discovery rate (FDR) <10%. The explained percentage by quantitative trait locus (QTL) to phenotypic variation was from 7.27 to 13.31%. Five of twenty five QTLs identified in this study were co-localized with the previously cloned genes or previously identified QTLs related to Al tolerance or root growth/development. These results indicated that landraces are important sources for Al tolerance in rice and the mapping results could provide important information to breed Al tolerant rice cultivars through marker-assisted selection.

Mining Beneficial Genes for Salt Tolerance From a Core Collection of Rice Landraces at the Seedling Stage Through Genome-Wide Association Mapping

“…In previous studies, the rice core collection was sequenced using the Specific-Locus Amplified Fragment Sequencing(SLAF-seq)approach and 67,511 SNPs were obtained ( Zhao et al, 2018 ). Based on them, 2,487,353 SNPs were further obtained by the imputation method of ( Wang et al, 2018b ).…”

“…Therefore, it is worth to perform GWAS with such a core collection for ST in rice. Population structure analysis for the core collection indicated that there existed two subgroups mainly corresponding to indica and japonica subspecies and the linkage disequilibrium (LD) decay distance was about 200–500 kb ( Zhang et al, 2011 ; Li and Zhang, 2012 ; Zhao et al, 2018 ). Using this core collection, several researches have been performed to identify resistant QTLs for aluminum (Al) tolerance and cold tolerance.…”

“…Using this core collection, several researches have been performed to identify resistant QTLs for aluminum (Al) tolerance and cold tolerance. With the mixed linear model, GWAS identified a total of 30 QTLs for Al tolerant traits which explained 7.73 to 13.30% of the phenotypic variation ( Zhao et al, 2018 ). A total of 26 QTLs were found to be significantly associated with cold tolerance, which explained 26–33% of the phenotypic variation ( Song et al, 2018 ).…”

High-LD SNP markers exhibiting pleiotropic effects on salt tolerance at germination and seedlings stages in spring wheat

“…Both significant levels allowed detecting markers with minor and large effects. Zhao et al ( 2018 ) reported QTL with R 2 ranged from 7.27 to 13.31% using p > 0.001 and 10% FDR in a rice GWAS panel tested under AL stress. At 20% FDR, minor effects of QTL associated with frost tolerance (R 2 < 10%) were detected and validated in two different genetic backgrounds of faba bean (Sallam et al 2016 ).…”

“…Both significant levels allowed detecting markers with minor and large effects. Zhao et al (2018) reported QTL with R 2 ranged from 7.27 to 13.31% using p > 0.001 and 10% FDR in a rice GWAS panel tested under AL stress.…”