Evolutionary Insights Based on SNP Haplotypes of Red Pericarp, Grain Size and Starch Synthase Genes in Wild and Cultivated Rice

Abstract

The origin and domestication of rice has been a subject of considerable debate in the post-genomic era. Rice varieties have been categorized based on isozyme and DNA markers into two broad cultivar groups, Indica and Japonica. Among other well-known cultivar groups Aus varieties are closer to Indica and Aromatic varieties including Basmati are closer to Japonica, while deep-water rice varieties share kinship to both Indica and Japonica cultivar groups. Here, we analyzed haplotype networks and phylogenetic relationships in a diverse set of genotypes including Indian Oryza nivara/Oryza rufipogon wild rice accessions and representative varieties of four rice cultivar groups based on pericarp color (Rc), grain size (GS3) and eight different starch synthase genes (GBSSI, SSSI, SSIIa, SSIIb, SSIIIa, SSIIIb, SSIVa, and SSIVb). Aus cultivars appear to have the most ancient origin as they shared the maximum number of haplotypes with the wild rice populations, while Indica, Japonica and Aromatic cultivar groups showed varying phylogenetic origins of these genes. Starch synthase genes showed higher variability in cultivated rice than wild rice populations, suggesting diversified selection during and after domestication. O. nivara/O. rufipogon wild rice accessions belonging to different sub-populations shared common haplotypes for all the 10 genes analyzed. Our results support polyphyletic origin of cultivated rice with a complex pattern of migration of domestication alleles from wild to different rice cultivar groups. The findings provide novel insights into evolutionary and domestication history of rice and will help utilization of wild rice germplasm for genetic improvement of rice cultivars.

Designing of a mini-core that effectively represents 3004 diverse accessions of rice

“…On the other hand, H4 haplotype showed inclination towards short grain trait, having the least mean grain length of 4.8 mm. Above, haplotype observation was similar to one recent study dissecting the separate clustering of grain length haplotypes for varying size and different rice groups (Singh et al, 2017).…”

Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor‐made rice with enhanced genetic gains

“…Recently, Singh et al . () investigated the SNP haplotype variation in GS3 gene for grain size (major grain size gene) in a set of 160 wild rice accessions that resulted in three major ( GS3 ‐H1, GS3 ‐H4, and GS3 ‐H9) and six minor ( GS3 ‐H2, GS3 ‐H3, GS3 ‐H5, GS3 ‐H6, GS3 ‐H7, and GS3 ‐H8) haplotypes.…”

“…Rice is the staple food for more than half of the population, and in the context of the rapidly increasing population, there is an obvious need to enhance grain yield under fluctuating climatic conditions. The advances in genomics and other allied fields render a great opportunity for translational research in plants (Varshney et al, 2014). Several key genes associated with rice grain yield and related traits have been functionally characterized in the past.…”

“…For example, haplotype diversity of GW2 locus was investigated in 93 indica and aromatic rice germplasm and based on the re-sequencing data of the GW2 locus four new SNPs were identified (Dixit et al, 2013). Recently, Singh et al (2017) investigated the SNP haplotype variation in GS3 gene for grain size (major grain size gene) in a set of 160 wild rice accessions that resulted in three major (GS3-H1, GS3-H4, and GS3-H9) and six minor (GS3-H2, GS3-H3, GS3-H5, GS3-H6, GS3-H7, and GS3-H8) haplotypes.…”

Genetic Effects of Soluble Starch Synthase IV -2 and It with ADPglucose Pyrophorylase Large Unit and Pullulanase on Rice Qualities

“…Compared with the other SSs, it contains a highly similar C-terminal region, which includes the catalytic and starchbinding domains, and a unique N-terminal region with several long coiled-coil motifs that have been implicated in protein-protein interactions (Cao et al, 1999). which plays an important role in determining starch granule morphology and maintaining amyloplast envelope structure (Singh et al, 2017). Spatio-temporal expression patterns analysis showed that SSIV-2 was mainly expressed in leaves and expressed consistently during grain filling, the transcript levels of SSIV-2 in endosperm were higher than that in pericarp.…”