Mapping QTL Conferring Grain Shape Traits And Stigma Exsertion Rate In Rice

The three grain shape factors, namely length, width and thickness, determine the1000-grain weight and appearance quality, while the 1000-grain weight is a key determinant of rice yield. Although hybrid rice has been commercialized, the relatively low outcrossing rate leads to a low rate of hybrid seed production and a relative high cost for hybrid seed production.As a result, the adoption of hybrid rice is limited in some parts of the world. Stigma exsertion is an important factor that influences the outcrossing ability of rice. In order to investigate the genetic basis of grain shape, 1000-grain weight and stigma exsertion, a QTL analysis, using SSR and chips,was performed using F2 and F3 populations derived from indica TGMS29 and temperature-sensitive genic male-sterile lines GZ63-4S in two consecutive years.With SSR detection in 2014 and 2015, five QTL for grain length were detected to be distributed on chromosomes 1, 2, 3, and 7, respectively. Among those, both the QTL located between RM1 and RM490 on chromosome 1 and the one located between RM240 and RM208 on chromosome 2 were repeatedly detected in the two years, and accounted for 21.3%, 22% and 12.8%, 15.7% of the phenotype variances in years of 2014 and 2015, respectively. Eight QTL for grain width were detected in two years, and located on chromosomes 1, 2, 3, 4, 7, and 9, respectively, explaining the variances ranging from 6.40% to 34.60%. Four QTL for grain thickness were detected on chromosomes 1, 3, and 7 in two years, among which the QTL flanked by RM251 and RM571 on chromosome 3 was stable in two years, accounting for 53.6% and 55% of the variance, respectively. Four QTL for 1000-grain weight were detected on chromosomes 1, 2, and 3. Of which the QTL located between RM220 and RM1 on chromosome 1 was stable in both years, and explained 15.1% and 15.4% of the phenotypic variances, respectively. Seven QTL for dual stigma exsertion rate were detected on chromosomes 3, 4, 5, 7 and 11 respectively, explaining the variances ranging from 6.06% to 67.30%. Six QTL for single stigma exsertion rate were detected on chromosomes 3, 4, 5, 7 and 11 respectively, accorading for the variances ranging from 7.80% to 53.40%.With chips detection in 2014 and 2015, eight QTL for grain length were detected and found to be distributed on chromosomes 1, 2 and 10, explaining the variances ranging from 0.02% to 24.02%. Nine QTL for grain width were detected in two years, and located on chromosomes 1, 2, 3, 4, 5, 7, 11, and 12, respectively, explaining the variances ranging from 1.99% to 28.54%. Eleven QTL for grain thickness were detected on chromosomes 1, 2, 3, 5, 7, 9 and 12, respectively, explaining the variances ranging from 3.05% to 35.77%. Ten QTL for 1000-grain were detected on chromosomes 1, 2, 4, 5, 7, 11 and 12, respectively, explaining the variances ranging from 0.88% to 20.77%. Nine QTL for dual stigma exsertion rate were detected on chromosomes 1, 2, 3, 4 and 6, respectively, explaining the variances ranging from 1.75% to 29.53%. Five QTL for single stigma exsertion rate were detected on chromosomes 1, 2, 3 and 6, respectively, explaining the variances ranging from 1.58% to 27.62%.These results could potentially be used for dissecting the genetic basis of grain shape, 1000-grain weight and stigma exsertion rate in the future experiments like fine mapping, cloning and breeding.