Genome-wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness.

Gopal Misra,Nese Sreenivasulu,Richard Mott,Olufunmilayo Ladejobi,Sabiha Parween,Saurabh Badoni,Hei Leung,Rakesh Kumar Singh

doi:10.1111/pbi.13516

Abstract

Rice varieties whose quality is graded as excellent have a lower percent grain chalkiness (PGC) of two per cent and below with higher whole grain yields upon milling, leading to higher economic returns for farmers. We have conducted a genome‐wide association study (GWAS) using a combined population panel of indica and japonica rice varieties, and identified a total of 746 single nucleotide polymorphisms (SNPs) that were strongly associated with the chalk phenotype, covered 78 Quantitative Trait Loci (QTL) regions. Among them, 21 were high‐value QTLs, as they explained at least 10 % of the phenotypic variance for PGC. A combined epistasis and GWAS was applied to dissect the genetics of the complex chalkiness trait, and its regulatory cascades were validated using gene regulatory networks. Promising novel epistatic interactions were found between the loci of chromosomes 6 (PGC6.1) and 7 (PGC7.8) that contributed to lower PGC. Based on haplotype mining only a few modern rice varieties confounded with a lower chalkiness, and they possess several PGC QTLs. The importance of PGC6.1 was validated through multi‐parent advanced generation intercrosses and several low‐chalk lines possessing superior haplotypes were identified. The results of this investigation have deciphered the underlying genetic networks that can reduce PGC to 2%, and will thus support future breeding programs to improve the grain quality of elite genetic material with high‐yielding potentials.

Highlights

Rice (Oryza sativa L.) is one of the oldest domesticated crops in Asia, originating from the wild rice species O. rufipogon
By conducting the genome-wide association study (GWAS) using ultra-dense single nucleotide polymorphisms (SNPs) that accounted for the population structure, 746 significant SNPs associated with the percent grain chalkiness (PGC), belonging to 77 different Quantitative Trait Loci (QTL), were identified from the different chromosomes, surpassing the Bonferroni threshold mark (−log10 (P) ≥ 7.68; red colour horizontal line) and the false discovery rate (FDR)-threshold criterion (P < 0.05) (Figure 1a, b, Table 1, Table S1)
Aside from identifying, the major QTLs that explain the higher phenotypic variation explained (PVE) through combined GWAS and epistasis, novel functional haplotypes were defined from the interacting QTLs of PGC6.1 (PVE = 27.53) and PGC7.8 (22.4–22.5 Mb region), and these were found to contribute to reducing the chalkiness to less than 2%

Summary

Introduction

Rice (Oryza sativa L.) is one of the oldest domesticated crops in Asia, originating from the wild rice species O. rufipogon. Chalkiness is considered undesirable in part, because it has a negative impact on the cooking quality of the rice (Butardo and Sreenivasulu, 2019) Overall, this undesirable trait has a negative influence on consumer acceptability and crop market value (Laborte et al, 2015; Siebenmorgen et al, 2013). This undesirable trait has a negative influence on consumer acceptability and crop market value (Laborte et al, 2015; Siebenmorgen et al, 2013) This trait is vital across the rice value chain, and it is crucial that natural variations in rice to reduce PGC are identified and utilized to improve elite highyielding lines, through breeding approaches

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Discussion

Conclusion