Genetic Interrogation Of Phenotypic Plasticity And Genome-enable Breeding Study In Cotton

Phenotypic plasticity,or the ability to adapt and thrive in changing climates and variable environments,is essential for developmental programs in plants.Despite its importance,the genetic underpinnings of phenotypic plasticity for key agronomic traits remain poorly understood in many crops.This study aimed to fill this gap by using genome-wide association study(GWAS)to identify genetic variations associated with phenotypic plasticity in upland cotton(Gossypium hirsutum L.).In this study,we collected genotype and phenotypic data from five terrestrial cotton populations to identify the sites associated with phenotypic plasticity by genome-wide association studies.We were able to predict terrestrial cotton phenotype and phenotypic plasticity through genome selection.Our results are as follows:(1)The study included 20 traits,such as yield,fiber quality,flowering date,and plant height.We identified 73 additive QTLs,32 dominant QTLs,and 6799 epistatic QTLs associated with these traits in five cotton populations.We categorized the epistatic QTLs into three groups(A_tA_t,A_tD_t,and D_tD_t)based on the subgroups where the two interaction sites are located,with A_tA_taccounting for 50.83%,A_tD_taccounting for 39.99%,and D_tD_taccounting for 9.18%.(2)We observed different trends in the changes of traits in in multiple environments,which indicates that phenotypic plasticity is widely present in upland cotton and has different effects on traits.We identified 117 additive QTLs,28dominant QTLs,and 4691 epistatic QTLs associated with phenotypic plasticity for 19traits in two populations with multi-year multipoint traits.Our results found that the genetic factors controlling mean phenotype and phenotypic plasticity are largely independent,suggesting that researchers have the potential to improve both mean phenotype and phenotypic stability.This could help select cotton accessions with high-quality phenotypes and plasticity levels appropriate to the target environment.(3)We combined all accessions of the five groups to obtain a population containing 2461 accessions.We analyzed the group structure of the population and divided it into three subgroups.We also drew the evolutionary tree of the group and calculated the LD decay of the population and the three subgroups.The LD decay of the population is approximately 501 kb.(4)We used the genome selection and combine the P value and LD distance of genome-wide association study results to find a genomic selection method suitable for upland cotton.We were able to achieve stable prediction of phenotypic plasticity and mean phenotype,and proposed a new method of cotton genome design breeding.We used seven models for prediction.In summary,our research provides new insights into the genetic basis of cotton phenotypic plasticity.By combining genomic selection,we were able to realize phenotypic and phenotypic plasticity prediction,and realize the first study of upland cotton genome design breeding.This provides a valuable possible for future upland cotton breeding study.