Abstract
Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding.
Highlights
Rice (Oryza sativa L.), a staple cereal crop, feeds more than half of the world’s population
We found head milled rice rate (HMRR) was negatively correlated with percentage of grains with chalkiness (PGWC) and Degree of endosperm chalkiness (DEC), which was consistent with the study of Zheng et al [58]
Wide ranges of genetic variations were present in the indica association panel for all 10 measured grain quality traits
Summary
Rice (Oryza sativa L.), a staple cereal crop, feeds more than half of the world’s population. Improvement of rice yield and grain quality is the major objective of rice breeding worldwide. Grain quality primarily includes grain appearance, milling, eating and cooking and nutrition qualities. Grain appearance quality mainly includes grain shape and chalkiness. Chalky grains, filled with loosely packed, round and large compound of starch granules, are more prone to breakage during milling and reduce head milled rice rate (HMRR). Milling quality determines the final yield and the broken kernel rate of the milled rice, which is of concern for consumers and farmers. Milling quality is measured by brown rice rate (BRR), milled rice rate (MRR) and HMRR. Brown rice is the de-hulled rice with the palea and lemma removed that can be used for cooking and eating. Among the above-mentioned three milling quality parameters, HMRR is the most important and greatly affects market value. HMRR depends on varietal characteristics, production factors, and harvesting, drying and milling processes
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