Assessment of the association between yield parameters and polymorphic sites of the <i>Ghd7</i> locus in a core-set of rice cultivars grown in Sri Lanka

Abstract

Yield improvement is a major aspect in rice breeding programs. Ghd7 is a pleiotropic gene which regulates yield, plant height, and heading date in rice. Although Ghd7 has been previously cloned and sequenced in several other rice cultivars, none of the studies have been conducted for Sri Lankan rice germplasm. Therefore, in this study, we assessed the yield performance of 12 rice cultivars, genetic polymorphism of Ghd7 locus and associations between DNA markers and yield traits. Breeder seeds of the selected cultivars were obtained from RRDI, Bathalagoda, and established under greenhouse conditions at Peradeniya, Sri Lanka in Maha and Yala seasons, 2017. The cultivars were subjected to morphometric analysis, genotyped for 12 DNA markers and sequenced at Seq7-8 locus. Morphometric data were subjected to single marker analysis using General Linear Model (GLM) in SAS 9.4. Here we reported six marker haplotypes based on the arrangement of 13 DNA maker alleles at Ghd7. Moreover, twenty-three SNP/INDEL variations at Seq7-8 locus revealed close genetic relationships between the rice cultivars Bg 90-2, Bg 352 and At 307, Bg310. Four polymorphic markers (Seq7-8, Seq1-2, RM5436 and RM5346) were significantly associated with rice yield traits so that they could be used in marker assisted selection. The SNPs/INDELs of Ghd7 were significantly associated with all the yield traits except 100 seed weight and 100 endosperm weight. Thus the present study demonstrate the possibility of employing marker assisted breeding to improve rice yield using the polymorphic genomic information at Ghd7 locus.Keywords: DNA markers for rice, Rice marker haplotypes, Pleiotropic genes in rice, Rice breeding in Sri Lanka, SNP and INDEL in rice breeding.

Application of Pedimap: a pedigree visualization tool to facilitate the decisioning of rice breeding in Sri Lanka

“…Yala season is generally drier 29 ), plant height, basal leaf sheath color, and additional color patterns, recommended type of the land, level of phosphorus deficiency tolerance, amount of brown rice recovery, milling recovery, head rice recovery, amylose content, gelatinization temperature, the weight of 1,000 grains, shape of the grain, pericarp color, the weight of a kg, the color of the buff coat and resistance/susceptibility to pests and diseases; brown planthopper (BPH), bacterial leaf blight and rice blast disease were recorded under phenotypic data ( Supplementary Table S1 online). The available DNA marker alleles, marker positions in the linkage map, and allelic scores were entered under molecular data [30][31][32][33] (Supplementary Table S2 online). pedimap procedure.…”