New SNP-Based Markers for Grain Chalk in Rice Identified By Whole Genome Sequencing and Selective Genotyping

High incidence of kernel chalk has greatly reduced U.S. long-grain quality of rice for farmers, millers and traders resulting in significant export decline and revenue loss. Recent introductions of hybrids and high temperatures during grain filling were deemed as major causes of chalky grains considered a complex trait controlled by numerous genes each with small effect. Several QTLs/genes have been reported to be associated with chalk, most of which are genotype dependent or discovered through mutation experiments. Goals of the research described here were to first identify and then evaluate candidate markers associated with chalkiness through development of allele-specific DNA markers from whole genome sequences of elite varieties with extreme chalk phenotypes. The SB5 mapping population was evaluated for chalk over two years in 2013 and 2014 in three Louisiana and Arkansas environments. Selective genotyping of 130 SNP markers of 20 low-chalk and 20 high-chalk lines from SB5 identified 24 SNPs significantly associated with chalk (R² 10% to 38%) across the three Louisiana and Arkansas environments. Validation experiments showed that selected candidate markers successfully predicted chalk phenotypes of all inbred lines tested. Genotyping of SB5 extremes with remaining polymorphic markers is ongoing with multivariate analyses to be performed to identify best marker combinations for marker-assisted breeding of low chalk in rice.