Genetic Analyses of Rice Grain Quality, Male Sterility and Wide Compatibility in Louisiana Hybrids

High yield and superior grain quality are utmost importance in a rice breeding program. The first objective of this research was to identify allele-specific DNA markers for endosperm chalk by analysis of SNP databases and selective genotyping (Experiment I) with subsequent marker evaluation among lines with diverse genetic backgrounds (Experiment II). Experiment I revealed 47 markers associated with chalk in at least one of three environments. Nineteen of these markers were considered stable while 14 were novel. Experiment II conducted in Louisiana and Arkansas in 2016 showed among 89 diverse lines, four common SNP markers for chalk on chromosomes 1, 2, and 12, three SNPs on chromosomes 2 and 6 for the SB5 subgroup, three SNPs on chromosomes 1, 9, and 10 for tropical japonica inbred lines, and five SNPs on chromosomes 1 and 3 for tropical japonica by indica RILs. Significant markers identified in this study may be used in genomic selection scheme to develop Louisiana varieties with low endosperm chalk. The second objective of the research was to identify and develop KASP-SNP markers as alternatives to SNP in male sterile 2009S using haplotype and linkage disequilibrium analyses. No SNP in this study completely distinguished male fertile from male sterile plants. However, two SNPs at the top of on chromosome 2 that differentiated two major haplotypes in adapted Louisiana japonica and indica germplasm may be used for indirect selection of male sterile lines. The third objective was to investigate association of wide compatibility gene S5n with yield and other agronomic characters. For lines with similar genetic background, S5nS5j hybrids produced significantly greater spikelet fertility and yield per plant than S5iS5j hybrids. Three genotypes (S5nS5n, S5iS5i and S5jS5j) were observed in U.S. and Louisiana hybrid parents. Long grain varieties carried S5nS5n while medium-grains exhibited S5jS5j. Male sterile and restorer lines showed mixtures of the three genotypes. Genotypes of testcrosses with low and high spikelet fertility confirmed the association of S5n with normal spikelet fertility in indica/japonica hybrids. S5nSi genotypes showed comparable spikelet fertility and yield to S5nS5n testcrosses. This study emphasized the need to breed and develop S5n male sterile and restorer lines to overcome potential indica-japonica hybrid sterility