Development and Utilization of Functional Kompetitive Allele-Specific PCR Markers for Key Genes Underpinning Fiber Length and Strength in Gossypium hirsutum L.

Lihua Li,Zhikun Li,Huifeng Ke,Yan Zhang,Zhiying Ma,Xingfen Wang,Zhengwen Sun,Liqiang Wu,Guiyin Zhang,Jun Yang

doi:10.3389/fpls.2022.853827

Abstract

Fiber length (FL) and fiber strength (FS) are the important indicators of fiber quality in cotton. Longer and stronger fibers are preferred for manufacturing finer yarns in the textile industry. Functional markers (FMs) designed from polymorphic sites within gene sequences attributing to phenotypic variation are highly efficient when used for marker-assisted selection (MAS) in breeding superior varieties with longer FL and higher FS. The aims of this study were to develop FMs via kompetitive allele-specific PCR (KASP) assays and to validate the efficacy of the FMs for allele discrimination and the potential value in practice application. We used four single-nucleotide polymorphism markers and 360 cotton accessions and found that two FMs, namely, D11_24030087 and A07_72204443, could effectively differentiate accessions of different genotypes with higher consistency to phenotype. The appeared frequencies of varieties harbored Hap2 (elite alleles G and T) with longer FL (> the mean of accessions with non-elite allele, 28.50 mm) and higher FS (> the mean of accessions with non-elite allele, 29.06 cN•tex–1) were 100 and 72.7%, respectively, which was higher than that of varieties harbored only on a single elite allele (G or T, 77.9 or 61.9%), suggesting a favorable haplotype for selecting varieties with superior FL and FS. These FMs could be valuable for the high-throughput selection of superior materials by providing genotypic information in cotton breeding programs.

Highlights

Upland cotton (Gossypium hirsutum L.) holds a predominant position as a cash crop by supplying largely natural fibers for the global textile industry (Paterson et al, 2012)
A panel comprising 360 upland cotton accessions was grown over eight environments to obtain the phenotypic characteristics of Fiber length (FL) and fiber strength (FS)
One single-nucleotide polymorphisms (SNPs) mutation, D11_24030087 (G/T), on the coding region of GhFL2 was detected to be significantly associated with FL

Summary

Introduction

Upland cotton (Gossypium hirsutum L.) holds a predominant position as a cash crop by supplying largely natural fibers for the global textile industry (Paterson et al, 2012). The deletions in the 5 untranslated region (UTR), intronic, and 3 UTR of GhFL2 were identified to be significantly associated with FL in our recent study (Ma et al, 2021) Another important gene, Gh_A07G1769, encoding chaperone DnaJ-domain superfamily protein, was deemed as a causal gene underpinning the FS of cotton (Ma et al, 2018). Three polymorphic single-nucleotide polymorphisms (SNPs) (A07_72203768, A07_72204322, and A07_72204443) were identified in the coding sequence of the gene resulting in the amino acid change from Val (V) to Ile (I), Thr (T) to Ser (S), and Lys (K) to Glu (E), respectively These two genes were suggested as target genes for selecting superior varieties in breeding programs. The utilization of these genes in breeding selection is still not in practice

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