Integration of QTL Mapping and Whole Genome Sequencing Identifies Candidate Genes for Alkalinity Tolerance in Rice (Oryza sativa)

Abstract

Soil alkalinity is an important stressor that impairs crop growth and development, resulting in reduced crop productivity. Unlike salinity stress, research efforts to understand the mechanism of plant adaptation to alkaline stress is limited in rice, a major staple food for the world population. We evaluated a population of 193 recombinant inbred lines (RIL) developed from a cross between Cocodrie and N22 under alkaline stress at the seedling stage. Using a linkage map consisting of 4849 SNP markers, 42 additive QTLs were identified. There were seven genomic regions where two or more QTLs for multiple traits colocalized. Three important QTL clusters were targeted, and several candidate genes were identified based on high impact variants using whole genome sequences (WGS) of both parents and differential expression in response to alkalinity stress. These genes included two expressed protein genes, the glucan endo-1,3-beta-glucosidase precursor, F-box domain-containing proteins, double-stranded RNA-binding motif-containing protein, aquaporin protein, receptor kinase-like protein, semialdehyde hydrogenase, and NAD-binding domain-containing protein genes. Tolerance to alkaline stress in Cocodrie was most likely due to the low Na+/K+ ratio resulting from reduced accumulation of Na+ ions and higher accumulation of K+ in roots and shoots. Our study demonstrated the utility of integrating QTL mapping with WGS to identify the candidate genes in the QTL regions. The QTLs and candidate genes originating from the tolerant parent Cocodrie should be targeted for introgression to improve alkalinity tolerance in rice and to elucidate the molecular basis of alkali tolerance.

Genetic Dissection of Alkalinity Tolerance at the Seedling Stage in Rice (Oryza sativa) Using a High-Resolution Linkage Map

“…The SNC QTLs, qSNC3, and qSNC6 [ 30 ] under alkaline stress had an overlapping region with qSNC3.32 and qRSR6.28 , respectively, detected in this study. Furthermore, qRKC3.32 and qSNC4.16 [ 36 ] also co-localized with qSNC.32 and qSKC4.16 of this study. A shoot K + conc.…”

“…The interval of qSKC1.13 QTL overlapped with relative root number QTL qRRN1 detected under alkaline stress [ 41 ]. Both qlogCHL1.28 and qDW1.38 co-localized with the qSHL1.38 identified in our previous study [ 36 ]. The QTLs, qlogSHL2.31 and qSNC2.32 located between 31–32 Mb position on chromosome 2 were present within the interval of earlier identified qDLR2-1 [ 34 ].…”

“…The QTLs, qSNC10.16 and qDW11.02, identified in this study had an overlapped interval with qRGE10 and qRGE11 , respectively [ 41 ]. A major QTL qSKC10.18 was also identified in the same genomic region in our previous study [ 36 ].…”

“…Both qlogSHL6.006 and qRSR6.28 were similar to the qDLR6-1 detected under alkaline stress [ 34 ]. The qDW8.12 and qDW8.27 had an overlapping region with qDSRs8-1 [ 35 ] and qSHL8.27 [ 36 ], respectively. The QTLs, qSNC10.16 and qDW11.02, identified in this study had an overlapped interval with qRGE10 and qRGE11 , respectively [ 41 ].…”

“…Another major QTL qSNC3 for alkaline stress tolerance explained 21% of phenotypic variation [ 30 ]. Few other studies reported QTLs at the germination and seedling stage of rice under alkaline stress [ 34 , 35 , 36 ]. Rice plants overexpressing the LSD1-like-type zinc finger protein OsLOL5 and nucleus-encoded thylakoid protein OsY3IP1 improved alkalinity tolerance [ 37 , 38 ].…”