Superior haplotypes towards development of low glycemic index rice with preferred grain and cooking quality

Abstract

Increasing trends in the occurrence of diabetes underline the need to develop low glycemic index (GI) rice with preferred grain quality. In the current study, a diverse set of 3 K sub-panel of rice consisting of 150 accessions was evaluated for resistant starch and predicted glycemic index, including nine other quality traits under transplanted situation. Significant variations were noticed among the accessions for the traits evaluated. Trait associations had shown that amylose content possess significant positive and negative association with resistant starch and predicted glycemic index. Genome-wide association studies with 500 K SNPs based on MLM model resulted in a total of 41 marker-trait associations (MTAs), which were further confirmed and validated with mrMLM multi-locus model. We have also determined the allelic effect of identified MTAs for 11 targeted traits and found favorable SNPs for 8 traits. A total of 11 genes were selected for haplo-pheno analysis to identify the superior haplotypes for the target traits where haplotypes ranges from 2 (Os10g0469000-GC) to 15 (Os06g18720-AC). Superior haplotypes for RS and PGI, the candidate gene Os06g11100 (H4-3.28% for high RS) and Os08g12590 (H13-62.52 as intermediate PGI). The identified superior donors possessing superior haplotype combinations may be utilized in Haplotype-based breeding to developing next-generation tailor-made high quality healthier rice varieties suiting consumer preference and market demand.

Figure 1

Overall methodology flow of the study to unravel the SNP associations, identifying favorable SNPs, locating the candidate genes and superior haplotype identification in transplanted rice (TPR) by haplotype based breeding to assemble superior haplotypes to design the rice varieties suitable for diabetics with improved grain quality parameters.

Figure 2

Investigation on correlation coefficients explaining associations among predicted glycemic index and resistant starch with rice quality parameters under transplanted rice system. AC—Amylose content, KL—Kernel length, KB—Kernel breadth, LBR—Length/ Breadth ratio, ASV—Alkali spreading value, KLAC—Kernel length after cooking, KBAC—Kernel breadth after cooking, LER—Linear elongation ratio, GC—Gel consistency, RS—Resistant starch, PGI—Predicted glycemic index, TPR—Transplanted rice. * Significance at p-value < 0.05, ** Significance at p-value < 0.01.

Figure 3

Genome wide association studies—Manhattan plot showing peak associations for resistant starch and predicted glycemic index in (a) Peak association for resistant starch on chromosome 2, 6 and 8 in transplanted rice, (b) Peak association for PGI on chromosome 1, 8 and 11 in transplanted rice.

Figure 4

(a) Haplotype variations observed for Os08g12590 associated with predicted glycemic index in TPR situation, (b) Boxplot shown haplotype diversity and variations exists between haplotypes of Os08g12590 linked with PGI with the significance level of p value < 0.05 and different alphabets denotes significant differences between haplotypes, (c) Assembly of superior haplotypes (Haplotype based breeding) of RS, PGI and other important quality traits with favorable allelic effect to design diabetic free healthy rice with preferred grain quality and genetic gains.