title: Mapping by sequencing in cotton (Gossypium hirsutum) line MD52ne identified candidate genes for fiber strength and its related quality attributes.
abstract: Three QTL regions controlling three fiber quality traits were validated and further fine-mapped with 27 new single nucleotide polymorphism (SNP) markers. Transcriptome analysis suggests that receptor-like kinases found within the validated QTLs are potential candidate genes responsible for superior fiber strength in cotton line MD52ne. Fiber strength, length, maturity and fineness determine the market value of cotton fibers and the quality of spun yarn. Cotton fiber strength has been recognized as a critical quality attribute in the modern textile industry. Fine mapping along with quantitative trait loci (QTL) validation and candidate gene prediction can uncover the genetic and molecular basis of fiber quality traits. Four previously-identified QTLs (qFBS-c3, qSFI-c14, qUHML-c14 and qUHML-c24) related to fiber bundle strength, short fiber index and fiber length, respectively, were validated using an F3 population that originated from a cross of MD90ne × MD52ne. A group of 27 new SNP markers generated from mapping-by-sequencing (MBS) were placed in QTL regions to improve and validate earlier maps. Our refined QTL regions spanned 4.4, 1.8 and 3.7 Mb of physical distance in the Gossypium raimondii reference genome. We performed RNA sequencing (RNA-seq) of 15 and 20 days post-anthesis fiber cells from MD52ne and MD90ne and aligned reads to the G. raimondii genome. The QTL regions contained 21 significantly differentially expressed genes (DEGs) between the two near-isogenic parental lines. SNPs that result in non-synonymous substitutions to amino acid sequences of annotated genes were identified within these DEGs, and mapped. Taken together, transcriptome and amino acid mutation analysis indicate that receptor-like kinase pathway genes are likely candidates for superior fiber strength and length in MD52ne. MBS along with RNA-seq demonstrated a powerful strategy to elucidate candidate genes for the QTLs that control complex traits in a complex genome like tetraploid upland cotton.
authors.affiliation: Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, 70124, USA.
authors.forename: Md S
authors.initials: MS
authors.lastname: Islam
authors.affiliation: Crop Genetics Research Unit, USDA-ARS, 141 Experiment Station Road, Stoneville, MS, 38772, USA.
authors.forename: Linghe
authors.initials: L
authors.lastname: Zeng
authors.affiliation: Cotton Chemistry and Utilization Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, 70124, USA.
authors.forename: Gregory N
authors.initials: GN
authors.lastname: Thyssen
authors.affiliation: Cotton Structure and Quality Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, 70124, USA.
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Delhom
authors.affiliation: Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, 70124, USA.
authors.forename: Hee Jin
authors.initials: HJ
authors.lastname: Kim
authors.affiliation: Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, 70124, USA.
authors.forename: Ping
authors.initials: P
authors.lastname: Li
authors.affiliation: Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, 70124, USA. david.fang@ars.usda.gov.
authors.forename: David D
authors.initials: DD
authors.lastname: Fang
mesh_terms: D002874:Chromosome Mapping; D032561:Cotton Fiber; D018744:DNA, Plant / Q000235:genetics; D017343:Genes, Plant; D008040:Genetic Linkage; D005819:Genetic Markers; D005838:Genotype; D003368:Gossypium / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers