Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton

Abstract

Background: The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization. Results: In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions: This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.

Quantitative Trait Locus Analysis and Identification of Candidate Genes for Micronaire in an Interspecific Backcross Inbred Line Population of Gossypium hirsutum × Gossypium barbadense

“…Therefore, it was still valid to carry out the current QTL analysis in the BIL population developed from the two parents. The results further showed that the two parents of different species possessed different genetic loci involved in MIC formation in that both parents had QTL alleles decreasing MIC (8 QTLs in CRI36 vs. 17 QTLs in Hai7124), consistent with many previous QTL studies in cotton (Lacape et al, 2010;Zhang et al, 2014Zhang et al, , 2020Zhu et al, 2020). As such, transgressive segregation in MIC was observed in that the BILs developed from the two parents had MIC ranging from 2.10 to 6.17, with an average BLUP of 4.18.…”

Identification of Candidate Genes for Lint Percentage and Fiber Quality Through QTL Mapping and Transcriptome Analysis in an Allotetraploid Interspecific Cotton CSSLs Population

“…Full utilization of genetic resources of G. barbadense with excellent fiber quality should be considered to promote genetic enhancement of widely cultivated G. hirsutum varieties (Zhu et al, 2020). Eight superior lines with the best comprehensive LP, FL, FS, and FM phenotypes in four environments were identified in the CSSLs population (Table 3).…”

Genetics, Breeding and Genetic Engineering to Improve Cottonseed Oil and Protein: A Review

“…Chromosomes or genes introduced to G. hirsutum from G. barbadense and other tetraploid Gossypium species were found to affect cottonseed oil content substantially, based on CSLs ( Wu et al, 2009 , 2010 ; Bellaloui et al, 2020 ; Saha et al, 2020 ). Multiple QTL alleles from G. barbadense were demonstrated as highly promising for enhancing seed oil content in introgressed G. hirsutum lines ( Zhu et al, 2020 ). Therefore, introgression breeding between G. hirsutum and G. barbadense may greatly improve the content of seed oil content and possibly fatty acid composition.…”