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.

Multi-model genome-wide association studies for appearance quality in rice

“…Increasing living standards underline the need to develop healthier high-quality rice ( Yu et al., 2013 ; Hori et al., 2015 ; Sahu et al., 2017 ; Wang et al., 2017 ; Misra et al., 2019 ; Meng et al., 2022 ) for traits such as color, aroma, lack of broken seed grains, grain length, and flavor. To meet consumer preferences and market demands, the development of tailored rice with preferred appearance quality is of utmost importance after rice yield enhancement ( Arite et al., 2009 ; Abbai et al., 2019 ; Selvaraj et al., 2021 ). Grain quality is a complex quantitative trait ( Yu et al., 2013 ; Hori et al., 2015 ; Misra et al., 2019 ; Meng et al., 2022 ) governed by manifold genes, and there is a large gap in our perception of the networks regulating grain quality in rice ( Li et al., 2022 ).…”

“…Cultivated rice ( Oryza sativa L.) is an important source of calories for more than half of the global population. With improved living standards and increasing awareness among people worldwide, there is a growing demand for the consumption of superior quality healthier rice varieties ( Bao, 2014 ; Adjah et al., 2020 ; Selvaraj et al., 2021 ; Hori and Sun, 2022 ). Therefore, high-quality rice has become a paramount consideration for rice breeders, consumers, and producers ( Qiu et al., 2021 ).…”

“…The crucial determinants of rice grain quality include appearance, milling, nutritional composition, aroma, and cooking properties. Recently, more efforts have been made to breed rice varieties with desirable traits in terms of higher head rice recovery (HRR, %), and lower percentage of chalky grains (PGC, %) by discovering key haplotype variations, thereby harnessing allelic diversity in the germplasm ( Selvaraj et al., 2021 ). Currently, molecular advances and genome sequencing platforms with lower costs have aided in cloning and functionally dissecting a series of genetic factors/quantitative trait loci (QTLs) in rice ( Varshney et al., 2014 ; Abbai et al., 2019 ).…”

Type‐2 Diabetes and Identification of Major Genetic Determinants of Glycemic Index in Rice – A Review

“…However, nowadays, people are more concerned about the health benefits of rice rather than the quality and, therefore, give more priority to rice varieties with high AC or low GI as it regulates blood glucose levels. [ 62 ] Understanding the molecular basis of AC variations in rice is crucial for breeders to develop superior rice varieties with low GI and suitable to the consumer's preference and market quality.…”

Reverse genetic approaches for breeding nutrient-rich and climate-resilient cereal and food legume crops

“…Thus, this study provided an opportunity to identify donors having superior haplotype combinations. These donors can be used for tailoring high quality healthier rice varieties based on consumer preference and market demand using haplotype-based breeding (Selvaraj et al 2021). Similarly, in pigeon pea, superior haplotypes for 10 drought-responsive candidate genes have been identified through whole genome re-sequencing of 292 genotypes.…”