Identification of Genomic Regions Controlling Chalkiness and Grain Characteristics in a Recombinant Inbred Line Rice Population Based on High-Throughput SNP Markers.

Abdulrahman Al-Hashimi,Charles Ruiz,Yheni Dwiningsih,Anuj Kumar,Jawaher Alkahtani,Julie Thomas,Andy Pereira

doi:10.3390/genes12111690

Abdulrahman Al-Hashimi, Charles Ruiz + Show 5 more

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https://doi.org/10.3390/genes12111690

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Abstract

Rice (Oryza sativa L.) is the primary food for half of the global population. Recently, there has been increasing concern in the rice industry regarding the eating and milling quality of rice. This study was conducted to identify genetic information for grain characteristics using a recombinant inbred line (RIL) population from a japonica/indica cross based on high-throughput SNP markers and to provide a strategy for improving rice quality. The RIL population used was derived from a cross of “Kaybonnet (KBNT lpa)” and “ZHE733” named the K/Z RIL population, consisting of 198 lines. A total of 4133 SNP markers were used to identify quantitative trait loci (QTLs) with higher resolution and to identify more accurate candidate genes. The characteristics measured included grain length (GL), grain width (GW), grain length to width ratio (RGLW), hundred grain weight (HGW), and percent chalkiness (PC). QTL analysis was performed using QTL IciMapping software. Continuous distributions and transgressive segregations of all the traits were observed, suggesting that the traits were quantitatively inherited. A total of twenty-eight QTLs and ninety-two candidate genes related to rice grain characteristics were identified. This genetic information is important to develop rice varieties of high quality.

Highlights

Accepted: 22 October 2021Rice (Oryza sativa L.) is the major dietary component for approximately more than half of the global population [1], and the demand for high-quality rice is gradually increasing due to the increasing standards of living [2]
According to our previous study of chalkiness and grain characteristics using diverse rice genotypes, we found that the upland japonica variety Kaybonnet and the indica variety ZHE733 displayed a significant difference in percent chalkiness
Significant differences for percent chalkiness (PC), grain length (GL), and RGLW were found between the two parents

Summary

Introduction

Accepted: 22 October 2021Rice (Oryza sativa L.) is the major dietary component for approximately more than half of the global population [1], and the demand for high-quality rice is gradually increasing due to the increasing standards of living [2]. The indicators of high-quality rice are based on physical characteristics and sensory properties such as milling performance, grain appearance, aroma, cooking, and nutrient composition [3]. These indicators are becoming important factors in rice marketing, which affects consumer acceptance of rice. Grain appearance quality is determined by grain length (GL), grain width (GW), grain length to width ratio (RGLW), hundred grain weight (HGW), and percent chalkiness (PC) or translucency [4]. Preference of rice quality is influenced by cultures and habits [5]. Slender and long grains having an RGLW of three or above are generally preferred by the majority of rice consumers in most Asian countries, including India, China, and Thailand

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