Combination of Eight Alleles at Four Quantitative Trait Loci Determines Grain Length in Rice

A Linear Regression Model for the Prediction of Rice Sheath Blight Field Resistance

Rice sheath blight (SB) disease is a global issue that causes great yield losses each year. To explore whether SB field resistance can be predicted, 273 rice genotypes were inoculated and evaluated for SB field resistance across nine environments from 2012 to 2019 to identify loci associated with SB resistance by association mapping. A total of 80 significant marker-trait associations were detected in nine environments, among which six loci (D130B, D230A, D304B, D309, D427A, and RM409) were repeatedly detected in at least two environments. A linear regression model for predicting SB lesion length was developed using genotypic data of these six loci and SB field resistance data of the 273 rice genotypes: y = 34.44 - 0.56x, where y is the predicted value of lesion length, and x is the total genotypic value of the six loci. A recombinant inbred line (RIL) population consisting of 219 lines that was grown in six environments (from 2013 to 2018) for evaluation of SB field resistance was used to check the prediction accuracy of the prediction model. The average absolute error between the predicted lesion length and real lesion length for the RIL population was 6.67 cm. The absolute errors between predicted and real lesion lengths were <6 cm for 51.22% of the lines and <9 cm for 71.22% of the lines. An SB visual rating prediction model was also developed, and the average absolute error between the predicted visual rating and real visual rating for the RIL population was 0.94. These results indicated that the rice SB lesion length can be predicted by the development of a linear regression model using both genotypic and phenotypic data.

Genetic dissection of grain traits in Yamadanishiki, an excellent sake-brewing rice cultivar

The grain traits of Yamadanishiki, an excellent sake-brewing rice cultivar in Japan, are governed by multiple QTLs, namely, a total of 42 QTLs including six major QTLs. Japanese rice wine (sake) is produced using brewing rice (Oryza sativa L.) that carries traits desirable for sake-brewing, such as a larger grain size and higher white-core expression rate (WCE) compared to cooking rice cultivars. However, the genetic basis for these traits in brewing rice cultivars is still unclear. We performed analyses of quantitative trait locus (QTL) of grain and days to heading over 3 years on populations derived from crosses between Koshihikari, a cooking rice, and Yamadanishiki, an excellent sake-brewing rice. A total of 42 QTLs were detected for the grain traits, and the Yamadanishiki alleles at 16 QTLs contributed to larger grain size. Two major QTLs essential for regulating both 100-grain weight (GWt) and grain width (GWh) were harbored in the same regions on chromosomes 5 and 10. An interaction was noted between the environment and the QTL associated with WCE on chromosome 6, which was detected in two of 3 years. In addition, two QTLs for WCE on chromosomes 3 and 10 overlapped with the QTLs for GWt and GWh, suggesting that QTLs associated with grain size also play an important role in the formation of white-core. Despite differences in the rate of grain growth in both Koshihikari and Yamadanishiki across 2 years, the WCE in Yamadanishiki remained consistent, thus demonstrating that the formation of white-core does not depend on grain filling speed. These data can be informative for programs involved in breeding better cooking and brewing rice cultivars.

Combination of twelve alleles at six quantitative trait loci determines grain weight in rice

Grain weight, which is controlled by quantitative trait loci (QTLs), is one of the most important determinants of rice yield. Although many QTLs for grain weight have been identified, little is known about how different alleles in different QTLs coordinate to determine grain weight. In the present study, six grain-weight-QTLs were detected in seven mapping populations (two F₂, one F₃, and four recombinant inbred lines) developed by crossing ‘Lemont’, a United States japonica variety, with ‘Yangdao 4’, a Chinese indica variety. In each of the six loci, one allele from one parent increased grain weight and one allele from another parent decreased it. Thus, the 12 alleles at the six QTLs were subjected to regression analysis to examine whether they acted additively across loci leading to a linear relationship between the predicted breeding value of QTL and phenotype. Results suggested that a combination of the 12 alleles determined grain weight. In addition, plants carrying more grain-weight-increasing alleles had heavier grains than those carrying more grain-weight-decreasing alleles. This trend was consistent in the seven mapping populations. Thus, these six QTLs might be used in marker-assisted selection of grain weight, by stacking different grain-weight-increasing or -decreasing alleles.