As a staple food for more than half of the world's population, the importance of rice is self-evident.Compared with ordinary rice, rice cultivars with superior eating quality and appearance quality are more popular with consumers due to its unique taste and ornamental value, even if their price is much higher. Appearance quality and CEQ (cooking and eating quality) are two very important aspects in the evaluation of rice quality. Here, we performed a genome-wide association study on chalkiness rate in a diverse panel of 533 cultivated rice accessions. We identi ed a batch of potential chalky genes and prioritize one (LOC_Os03g48060) for functional analyses. Two oury outer endosperm mutants ( o19-1 and o19-2) were generated through editing LOC_Os03g48060 (named as FLO19 in this study), which encodes a class I glutamine amidotransferase. The different performance of the two mutants in various storage substances directly led to completely different changes in CEQ. The mutation of FLO19 gene caused the damage of carbon and nitrogen metabolism in rice, which affected the normal growth and development of rice, including decreased plant height and yield loss by decreased grain lling rate. Through haplotype analysis, we identi ed a haplotype of FLO19 that can improve both CEQ and appearance quality of rice, Hap2, which provides a selection target for rice quality improvement, especially for high-yield indica rice varieties.
As a staple food for more than half of the world’s population, the importance of rice is self-evident. Compared with ordinary rice, rice cultivars with superior eating quality and appearance quality are more popular with consumers due to its unique taste and ornamental value, even if their price is much higher. Appearance quality and CEQ (cooking and eating quality) are two very important aspects in the evaluation of rice quality. Here, we performed a genome-wide association study on chalkiness rate in a diverse panel of 533 cultivated rice accessions. We identified a batch of potential chalky genes and prioritize one (LOC_Os03g48060) for functional analyses. Two floury outer endosperm mutants (flo19-1 and flo19-2) were generated through editing LOC_Os03g48060 (named as FLO19 in this study), which encodes a class I glutamine amidotransferase. The different performance of the two mutants in various storage substances directly led to completely different changes in CEQ. The mutation of FLO19 gene caused the damage of carbon and nitrogen metabolism in rice, which affected the normal growth and development of rice, including decreased plant height and yield loss by decreased grain filling rate. Through haplotype analysis, we identified a haplotype of FLO19 that can improve both CEQ and appearance quality of rice, Hap2, which provides a selection target for rice quality improvement, especially for high-yield indica rice varieties.
Hybrid sterility is the major obstacle to the utilization of inter-subspecific heterosis in hybrid rice breeding. The S5 locus, composed of three adjacent genes ORF3, ORF4, and ORF5, plays a crucial role in regulating indica/japonica hybrids’ female sterility. Through a series of crosses involving 38 parents, three alleles of S5, ORF3+ORF4−ORF5n, ORF3+ORF4+ORF5n, and ORF3−/ORF4−/ORF5n, all could be regarded as wide-compatibility alleles, and when crossed with indica or japonica rice, they all showed significantly high fertility. Then, in order to explore the genes’ function, we further knocked out genes by using CRISPR/Cas9-based genome editing. Our results demonstrate that the ORF3+ was not just the protector in the killer-protector system, and knocking out ORF3 of the indica allele seriously affected the rice’s normal development. We observed the concrete enhancing hybrid spikelet fertility from the crosses between the ORF4+ knockout japonica materials with indica varieties. By conducting the comparative RNA-Seq analysis of young spikelets, we found that the ORF4+/ORF4− could modulate the hybrid fertility by affecting the expressions of genes related to the function of the Golgi apparatus. This study indicated that knocking out the ORF4+ of the japonica allele or using the alleles carrying ORF5n would provide effective approaches to overcome indica/japonica hybrid female sterility in rice breeding.
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