Dissection Of Genetic Variation Underlying Weeping Traits In Prunus Mume Sieb.et Zucc.Based On Genome-wide Association Study And QTL Mapping

Mei?Prunus mume Sieb.et Zucc.?,belonging to Prunus of Rosaceae,has greatly cultural and economic value.Weeping P.mume is a kind of cultivars with weeping branch traits,which has gained much attention for its unique ormamental value.However,the genetic variation of weeping traits is still unclear.Revealing the genetic variation of weeping P.mume will accelerate the breeding of weeping P.mume.In this study,we combined genome-wide associated study?GWAS?,quantitative trait locus?QTL?mapping,and RNA-seq analysis to reveal the variation of weeping traits in P.mume.Main results are as follows:?1?Phenotypic observation indicated that the weeping phenotype occurred indepently in shoot apical meristem,not affected by signaling molecules from upright trees and stocks.We observed that IAA treatments applied to the abaxial surface of the stem prominently altered the stem growth trajectory.With respect to their histological anatomy,we found the abnormal development of secondary structure in elongating stem of weeping trees,and the loss of phloem fibres.Seven sub-traits measured by using nested phenotypic method showed significant positive correlation,indicating that these sub-traits can represent the characteristics ofweeping traits.?2?QTL mapping identified six major QTLs for seven weeping traits mapped to LG7?Chr7?positioned at the range of 69.25-76.74 cM?9.61-11.57 Mb?explained 10.8-55.3%of the phenotypic variation,and ten minor QTLs mapped to the other four LGs?LG2,LG3,LG4,and LG5?explained 1.2-5.1%of the phenotypic variation.We identified fifty-five epistatic pairs?LOD>3,PVE>3%?and explained phenotypic variation ranging from 3%-31.6%.Epistatic pairs located in?near?the major QTL loci explained most of phenotypic variation.?3?Two major loci?BW7.1 and BW7.2?were detected on chromosome 7 using GWAS,which located at 11.1-11.8 Mb and 14.1-15.5 Mb,respectively.BW7.1 locus overlapped with major QTL.Finally,by integrating the GWAS peak,genome selection peak,and QTL peak we further narrowed down the majoroeffect QTL interval,which was located within the 11.06-11.32 Mb region on chromosome 7?defined as Pm WEEP?and included 37 candidate genes.?4?For the validation of the SNPs located in PmWEEP,we detected a core SNP?Chr7₁118291?,which showed the highest genotype frequency?96.3%?in weeping sub-population.The validation of SLAF markers commonly exhibited higher detection efficiency in Pm WEEP regions.Validated 11.03-11.32 region on chromosome 7 was tightly linked to weeping trait.These two results further eonfirmed that the PmWEEP candidate locus was reliable.?5?Based on transcriptome analysis,we identified only Pm0242I3 gene specifically and differentially expressed in the buds and stems of weeping P.mume.This gene was very close to the core SNP??9 kb?.RT-qPCR further validated the specific expression of Pm024213 in weeping P.mume.Functional annotation and analysis showed that Pm024213 was predicted to encode a putative thioredoxin protein.We further detected the DEGs co-expressed with Pm024213,and a hypothetical model was proposed for the regulatory networks involved in mei weeping branches in terms of auxin levels and lignin biosynthesis cues.In summary,we deciphered the parts of weeping traits formation,uncovered the major QTL loci and major putative genes controlling weeping traits,and proposed a hypothetical model of the regulatory networks.Thus,results of this study are of great significance in theoretical and practical field to reveal the genetic architecture of weeping traits and molecular marker-assisted breeding of weeping P.mume.