Tifeng Yang†, Haiyong Gu†, Wu Yang, Bin Liu, Shihu Liang* and Junliang Zhao*

Rice

Abstract

BackgroundGrain shape is a key trait in rice breeding. Although many QTLs and genes of grain shape have beenidentified, how different combinations of alleles of these genes affect grain shape is largely unknown. It is importantto understand the effects of grain shape gene combinations for breeding by design. In the present study, we performedgenetic dissection of the grain shapes in Guangdong Simiao varieties, a popular kind of rice in South China, toidentify the effective alleles and their combination for breeding.

ResultsWe selected two hundred nineteen indica accessions

with diverse grain shapes and fifty-two GuangdongSimiao varieties with long and slender grain shapes for genome-wide selection analysis. The results showed that four(GS3, GS5, GW5 and GL7) of the twenty grain shape genes fall into the regions selected for in Guangdong Simiao varieties.Allele analysis and frequency distribution of these four genes showed that GS3allele3 and GW5allele2 accounted for96.2%, and GL7allele2 and GS5allele2 accounted for 76.9% and 74.5% of the Simiao varieties, respectively. Further analysisof the allelic combinations showed that 30 allelic combinations were identified in the whole panel, with 28 alleliccombinations found in the international indica accessions and 6 allelic combinations found in Guangdong Simiaovarieties. There were mainly three combinations (combinations 17, 18 and 19) in the Guangdong Simiao varieties, withcombination 19 (GS3allele3 + GW5allele2 + GL7allele2 + GS5allele2) having the highest percentage (51.9%). All three combinationscarried GS3allele3 + GW5allele2, while combinations 17 (GL7allele1) and 19 (GL7allele2) showed significant differencesin both grain length and length/width ratio due to differences in GL7 alleles. Pedigree analysis of Guang8B, themaintainer of the first released Simiao male sterile line Guang8A, showed that the parent lines and Guang8B carriedGS3allele3 + GW5allele2 + GS5allele2, while the GL7 allele differed, resulting in significant differences in grain size.

ConclusionThe results suggest that specific alleles of GS3, GS5, GW5 and GL7 are the key grain shape genes usedin the Guangdong Simiao varieties and selected for grain shape improvement. Combination 19 is the predominantallelic combination in the Guangdong Simiao varieties. Our current study is the first to dissect the genetics of grainshape in Guangdong Simiao varieties, and the results will facilitate molecular breeding of Guangdong Simiao varieties.

KeywordsGuangdong Simiao varieties, Grain shape, Fixation index, Allele mining, Molecular breeding, Rice

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