| Interspecific hybridization expanded the genetic diversity and improved the key traits in crops.Upland cotton?cultivated G.hirsutum?is one of the most important economic crops worldwide and the primary source of natural fiber in the textile industry.Understanding the effects of introgressed fragments from exotic species on adaptability and fiber quality is significant for assisting breeding practices in cotton.This study systematically analyzes the genetic diversity,population structure,introgression events,and trait-associated loci in two populations to reveal the effects of introgression on population differentiation and fiber quality.The results are summarized as follows.Using Restriction site-associated DNA sequencing technology?RAD-seq?to analyze the genetic diversity and population structure of 582 tetraploid cottons,we found significantly higher genetic diversity corresponding landraces(?=0.041×10-3)than Upland cotton cultivars(?=0.022×10-3).In contrast with the previous categorization of landraces,we observed admixed ancestry of landraces.Although the genetic diversity of Upland cotton populations was lower than landraces,it could also be screened out two specific subgroups.Among them,the accessions of Group-2 were early-maturing and mainly cultivated in the high-latitude regions.The accessions of Group-1 were mainly cultivated in the low-latitude regions.Subgroup comparisons revealed that the divergence of Group-1 and Group-2 might have been induced by the extensive haplotype polymorphism on chromosome A08 and A06,respectively.A genome-wide association study?GWAS?confirmed that maturity-related locus existed in the divergent region on chromosome A06.Hence,we suggested that these extensive variations on both chromosomes might be related to adaptability in Upland cotton.Analysis of the whole population genotype demonstrated that all known haplotypes on chromosome A06 and A08 should form in landraces.These haplotypes might transfer to cultivars from landraces via two possible manners.One possibility was that the multiple haplotypes in cultivars were inherited from multiple landraces.Another was that only one haplotype of one landrace transferred to one cultivar and further hybridized with other landraces carried other haplotypes.Along with the cultivation shifting to the Xinjiang region,understanding the genomic basis of adaptability could be the foundation for identifying adaptive locus/genes,and maintaining the polymorphism of A06 and A08 chromosomes in Upland cotton cultivars will also be a benefit to preserve the extensive adaptability of G.hirsutum in China.By using GWAS and QTL mapping strategies in the Upland cotton population with 1,245 accessions,we identified 4,3,and 3 favorable alleles related to fiber length?FL2,FL3,FL4,and FL5?,fiber strength?FS1,FS2,and FS3?,and fiber elongation rate?FE1,FE2,and FE3?,respectively.Among them,FL3/FS2 and FL5/FS1 were pleiotropic alleles,enhancing fiber length and fiber strength.Furthermore,FL3/FS2,FL4,and FS3 were firstly reported in this study.For fiber length and fiber strength,the most frequent allele was FL2,accounting for over 75%.Both FL4 and FL5/FS1 were lower than25%,FL3/FS2 and FS3 were lower than 10%.The favorable alleles with lower frequency likely have a more significant phenotype improving effect.For instance,FL3/FS2 had a 15%improving effect on fiber length and fiber quality,but the improving effect of FL2 on fiber length was only 4.3%.This result demonstrated that most of the Upland cotton germplasm carried only FL2 and none of the favorable alleles for fiber strength,and FL3/FS2 only existed in a small number of introgression lines,which led to being lack of available gene resource and the bottleneck of fiber quality genetic improvement in modern Upland cotton.By analyzing the introgression events of thirteen exotic cotton species in 2,927 G.hirsutum accessions,we found that three exotic species with the most abundant introgressed fragments in the G.hirsutum genome were G.barbadense,G.arboreum,and G.thurberi,respectively.This result was consistent with documented records that G.barbadense and Pee Dee germplasm?developed from a triple-hybrid strain,G.arboreum×G.thurberi×G.hirsutum?were the primary sources of fiber-quality improvement of Upland cotton.By integrating fiber-quality GWAS results,we found that the fiber-quality favorable alleles came from various sources.FL2,FL5/FS1,and three fiber elongation rate alleles?FE1,FE2,and FE3?originated from G.hirsutum landraces.FL4 was a single base mutation in the exon of NAC029?A10G233100?,which introduced a stop codon.We also found that this mutation occurred within the cultivated G.hirsutum population.We found that FL3/FS2 and FS3 were exotic alleles introgressed from diploid cottons G.arboreum and G.thurberi,respectively.Although G.barbadense had the most abundant introgressed fragments in the cultivated G.hirsutum genome,no fiber-quality related favorable allele originated from G.barbadense.This result demonstrated that the fiber-quality alleles from G.barbadense were not common in cultivated G.hirsutum at least,perhaps only limited elite germplasm carried them.Evaluating all favorable alleles'pyramiding effect showed that the fiber quality of accessions carrying FL3/FS2 and FS3 was superior to others.Therefore,we suggested that the newly discovered alleles FL3/FS2 and FS3 were the keys to break the bottleneck of fiber-quality improvement in Upland cotton.However,both exotic alleles occupied a wide range of genomic regions because of the linkage drag,which caused the imperfection of yield traits.Therefore,a sizeable segregated population should be constructed to fine-map the causal variations/genes to break the disadvantageous linkage in the future.However,the favorable alleles controlling plant architecture,fiber yield,and maturity should be further identified based on a similar strategy.By analyzing the pyramiding effect of the target traits,the excellent allelic combination could be screened that considers quality,yield,and maturity for molecular breeding of cotton. |
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