Bridging sd1 molecular knowledge with recent breeding strategies for the improvement of traditional rice varieties - a japonica case-study

The rice semidwarfing gene, sd1, also known as the “green revolution gene”, has been studied intensively due to its contribution to the increase of crop production. Although sd1 breeding was extensively applied since the 1960s, the recent advances in the molecular basis of this gene alloweddesigning a more precise breeding strategy - marker assisted backcrossing (MAB) - to track sd1 introgression in two traditional rice varieties. For selection of sd1 plants we first confirmed the efficiency of specific markers based on Os200 x 2 gene sequence. Background selection was alsoperformed with the help of microsatellites markers (SSR) and a total of 7 breeding lines were recovered containing a higher percentage of recurrent parent genome (RPG). Analysis of Covariance (ANCOVA) using mean progenitor plant height as covariate was performed to compare several agronomic and quality-related parameters in two different environments. The results suggest that plant height differs significantly between the two environments F(1, 220) = 155.336; p < 0.001. From the total variability ofplant height we could conclude that 73% is due to the genotype, while 10.4% depends on the environment. In addition, the percentage of RPG seems negatively correlated with plant height (p < 0.005). MAB and background selection thus revealed as useful tools to assist breeding forsemidwarfism in traditional rice varieties

Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.)

Stigma and spikelet characteristics play an essential role in hybrid seed production. A mini-core of 90 accessions developed from USDA rice core collection was phenotyped in field grown for nine traits of stigma and spikelet and genotyped with 109 DNA markers, 108 SSRs plus an indel. Three major clusters were built upon Rogers’ genetic distance, indicative of indicas, and temperate and tropical japonicas. A mixed linear model combining PC-matrix and K-matrix was adapted for mapping marker-trait associations. Resulting associations were adjusted using false discovery rate technique. We identified 34 marker-trait associations involving 22 SSR markers for eight traits. Four markers were associated with single stigma exsertion (SStgE), six with dual exsertion (DStgE) and five with total exsertion. RM5_Chr1 played major role indicative of high regression with not only DStgE but also SStgE. Four markers were associated with spikelet length, three with width and seven with L/W ratio. Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 associated with all three correlated spikelet traits. The co-association should improve breeding efficiency because single marker could be used to assist breeding for multiple traits. Indica entry 1032 (cultivar 50638) and japonica entry 671 (cultivar Linia 84 Icar) with 80.65 and 75.17% of TStgE, respectively are recommended to breeder for improving stigma exsertion

Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome

The domestication of Asian rice (Oryza sativa) was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers.In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV) consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations.Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species