Abstract
Asian and African rice gene pools vary in many traits that are important in rice breeding. The genetic basis of these differences was evaluated by analysis of important agronomic traits in crosses between African and Asian rice. Trait-associated variants (TAVs) influencing three quantitative agronomic traits, heading date (Hd), tiller number at maturity (T), and 1000 grain weight (TGW), were identified by association analysis of crosses between Asian and African rice. Populations were developed by crossing WAB56-104 (Oryza sativa) and CG14 (Oryza glaberrima). DNA from plants with extremely high or low values for these phenotypes was bulked and sequenced. The reference genome of O. sativa cv Nipponbare was used in general association analysis and candidate gene analysis. A total of 5152 non-synonymous single nucleotide polymorphisms (SNPs) across 3564 genes distinguished the low and the high bulks for Hd, T, and TGW traits; 611 non-synonymous SNPs across 447 genes were found in KEGG pathways. Six non-synonymous SNPs were found in the sequences of LOC107275952, LOC4334529, LOC4326177, LOC107275432, LOC4335790, and LOC107275425 genes associated with Hd, T, and TGW traits. These genes were involved in: abscisic-acid biosynthesis, carotenoid biosynthesis, starch and sucrose metabolism, and cytokinin biosynthesis. Analysis of 24 candidate genes associated with Hd, T, and TGW traits showed seven non-synonymous variations in the sequence of Hd3a and Ehd2 from the Hd genes (not in a KEGG pathway), D10 and D53 from the T genes (strigolactones biosynthetic pathway), and Gn1a and GIF1 from the TGW genes (cytokinin biosynthetic and starch and sucrose metabolism pathways). This study identified significant differences in allele frequencies supported by high sequence depth in analysis of bulks displaying high and low values for these key traits. These trait-associated variants are likely to be useful in rice improvement.
Highlights
Rice is one of the world’s most important cereal crops and the staple food for more than half of the world’s population [1]
Thereafter, about 81% of the trimmed reads, a total of 798 million reads, were mapped against the O. sativa cv Nipponbare (IRGSP-1.0, NCBI) genome; the coverage ranged between 41× and 54× at this stage (Table S1)
The next-generation sequencing (NGS)-based bulk segregant analysis (BSA) approach has been proposed to overcome this limitation. The advantage of this approach is the ability to minimise the number of individuals to be genotyped and the ability to detect even loci of small effect by enriching rare alleles and boosting their effects [51]
Summary
Rice is one of the world’s most important cereal crops and the staple food for more than half of the world’s population [1]. The rapid escalation of the world population over the thirty years requires an increase in the production of cereal grains, including rice, to meet food demand. Increased production may be achieved by improvements in agronomically important traits through introgression or hybridisation. Key traits include heading date (Hd) (flowering time) and grain yield, which is determined by tiller number (T), 1000 grain weight (TGW), and grain number (Gn) [2,3,4,5]. One of the early crop domestication traits studied was flowering time or heading date for rice Numerous recent studies have reviewed in detail the available information on these traits for use in plant breeding [6,7,8,9,10].
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