Abstract
The textural attributes of cooked rice determine palatability and consumer acceptance. Henceforth, understanding the underlying genetic basis is pivotal for the genetic improvement of preferred textural attributes in breeding programs. We characterized diverse set of 236 Indica accessions from 37 countries for textural attributes, which includes adhesiveness (ADH), hardness (HRD), springiness (SPR), and cohesiveness (COH) as well as amylose content (AC). A set of 147,692 high quality SNPs resulting from genotyping data of 700K high Density Rice Array (HDRA) derived from the Indica diversity panels of 218 lines were retained for marker-trait associations of textural attributes using single-locus (SL) genome wide association studies (GWAS) which resulted in identifying hotspot on chromosome 6 for AC and ADH attributes. Four independent multi-locus approaches (ML-GWAS) including FASTmrEMMA, pLARmEB, mrMLM, and ISIS_EM-BLASSO were implemented to dissect additional loci of major/minor effects influencing the rice texture and to overcome limitations of SL-based GWAS approach. In total 224 significant quantitative trait nucleotide (QTNs) were identified using ML-GWAS, of which 97 were validated with at least two out of the four multi-locus methods. The GWAS results were in accordance with the very significant negative correlation (r = −0.83) observed between AC and ADH, and the significant correlation exhibited by AC (r < 0.4) with HRD, SPR, and COH. The novel haplotypes and putative candidate genes influencing textural properties beyond AC will be a useful resource for deployment into the marker assisted program to capture consumer preferences influencing rice texture and palatability.
Highlights
Texture is an important attribute of consumer’s acceptance criteria and quality evaluation of texture is a critical step in breeding
amylose content (AC) exhibited a high negative correlation with ADH (r = −0.83, P = 2.2E−16), which supports the fact that low amylose rice accessions tends to be stickier (Figure 1)
AC was considered as a key selection criterion for predicting cooked rice texture in normal breeding practices, HRD showed weak positive correlation with AC (r = 0.39, P = 3.05E−09)
Summary
Texture is an important attribute of consumer’s acceptance criteria and quality evaluation of texture is a critical step in breeding. High range of phenotypic textural variability exist in rice which are described as sticky, soft, dry, firm, and hard. These textural attributes appeals to be of interest to different segment of rice consumers across the globe (Kaosa-Ard and Juliano, 1991). Japanese and Chinese like the soft or sticky short rice grain, while consumers from Middle East, United States and the Latin America prefer non-sticky firm rice. While the widely preferred target of consumers of India and Pakistan favor soft and fluffy rice varieties (Lyon et al, 2000; Champagne et al, 2010), consumers from Bangladesh, Sri Lanka, Indonesia and Myanmar prefer hard textured rice varieties
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