Mining Of Lodging Resistance Genes By Linkage And Association Mapping In Rice(Oryza Sativa L.)

Rice is one of the major crops playing a crucial role to feed the world’s increasing population.Rice grain and its products are not only contributing to calorific intake but also the part of huge international trade.In near future it is needed to enhance the overall productivity of cereal grains including rice.Lodging is one of the factors that cause yield losses.It also cause reduction in mechanical harvesting efficiency and deteriorated grain quality.Along with increasing yield potential of cultivated rice,it is also required to minimize the grain losses.Lodging resistance is contributed by various genetic and environmental factors.To achieve the maximum resistance against lodging the standard cultural practices should be accompanied with potentially resistant genotypes.In a previously published project,a population of 3000 genotypes was used to produce a second generation of high-throughput sequence with 8 to 13 fold coverage by Illumina sequencing of whole-genome.For this study,a natural population was developed by selection of 795 sequenced and globally diverse genotypes.The genome wide distributed SNP markers with an average density of 12.3 SNPs per kb were extracted and used for association mapping.The high resolution phenotyping with seven lodging resistance traits was performed and the average data were used for genome wide association study.The association analysis was performed by two models(GLM and cMLM)by using three populations(whole population,indica and japonica subpopulations).Resultantly,a total 542 QTLs were mapped.Among them,157 QTLs were co-localized for different traits.The 98,32,16 and 11 target positions in whole rice genome were observed to control the 2,3,4 and 5 lodging related traits simultaneously.These results not only provide the better understanding about physical and biological correlation among various lodging resistance related traits but also provide handful knowledge about their corresponding positions in whole genome.These QTLs information can further confirm by development of bi-parental populations.By using the bi-parental population and BSA based strategy,we screened the 2368 SSR markers against parental DNA and identified the 126 polymorphic markers.Then,the extracted DNA of five thick-culm plants and five thin-culm plants were bulked separately to construct a bulked segregant reagent.This bulked DNA was used to screen the 126 selected SSR markers.Finally,fifty-one polymorphic markers on nine chromosomes were selected.The genetic map of 51 markers was able to reduce the genetic distance of various known QTLs.Furthermore,two new QTLs on chromosome 3 and 6 named as qWT1 and qST1 were identified by primary QTL mapping.By using the advanced and enlarged populations,the qST1 locus was fine mapped to a narrow region harboring a single gene Os06g0251700.The sequence comparison between two parents for subject gene locus revealed a premature stop codon in exon-6 and 30 substitutions in promoter region.The candidate locus was annotated for myosin-II heavy chain like proteins.According to online expression data base,it mainly expressed at the time of leaf sheath vegetative growth and shoot ripening.Both leaf sheath development and shoot strength at maturity are important contributors to the lodging resistance.The detailed functions of identified gene can be evaluated by cloning and genetic transformation in future studies.Lodging is also can consider as an abiotic stress which results in yield reduction.Therefore,lodging resistance as a favorable trait may have been played a role in domestication of cultivated rice species.The two lodging resistance confirming genes SCM2 and fcl were evaluated for nucleotide diversity and rice evolution.The evolutionary study of SCM2 revealed the purifying selection while fcl indicated the balanced selection in rice species.The haplotype analysis,phylogenetic tree and geographical distribution of different haplotypes showed the evolution of cultivated rice from a common ancestor O rufipogon.The plant dry matter contents and its chemical composition is one of the strength contributing factors in plant culm.Lignin,cellulose and hemicellulose contents were estimated in total dry matter of 410 diverse genotypes.The cellulose contents were observed to significantly associate with lodging resistance parameters specially the culm thickness traits as culm outer and inner diameter,culm wall thickness,section modulus and culm stiffness.It also exhibited a better association with pushing resistance and bending moment.The other chemical contents as K,Ca,P and Fe were estimated and there was a negative correlation among these chemical contents and lodging related traits.Three parameters of mechanical strength were also observed.The bending elasticity showed a negative while culm stiffness revealed significant positive correlation with lodging related traits.The tensile strength did not have any correlation with other traits except positive relation with culm stiffness and negative correlation with cLr.