Abstract
Cotton is an important economic crop in worldwide. It produces fiber for the textile industry and provides cottonseeds with high-quality protein and oil. However, the presence of gossypol limits the utilization of cottonseed. Two pairs of cotton near isogenic lines (NILs) with different pigment glands, i.e., Coker 312 vs Coker 312 W and CCRI12 vs CCRI12W, exhibit different gossypol contents. The glandless traits of Coker 312 W and CCRI12W are controlled by recessive and dominant genes, respectively. However, knowledge regarding the genomic variations in the NILs is limited. Therefore, the NILs genomes were resequenced and the sequencing depths were greater than 34×. Compared with the TM-1 genome, numerous SNPs, Indels, SVs, and CNVs were discovered. KEGG pathway analysis revealed that genes with SNPs and Indels from the recessive NILs and genes with Indels from the dominant NILs shared only one enriched pathway, i.e., the sesquiterpenoid and triterpenoid biosynthesis pathway, which is relevant to gossypol biosynthesis. Expression analysis revealed that key genes with variations that participate in the gossypol biosynthesis and pigment gland formation pathways had different expression patterns among the dominant, recessive glandless and glanded plants. The expression levels in the glanded organs were higher than those in their NILs. Altogether, our results provide deeper insight into cotton NILs with different pigment glands.
Highlights
IntroductionIn addition to producing nature fiber for the textile industry, cotton provides a large quantity of cottonseeds containing high-quality protein and oil[1]
Cotton (Gossypium spp.) is a leading economic crop worldwide
Gene Ontology (GO) annotation was conducted, and the results showed that the genes with single nucleotide polymorphisms (SNPs) and Indels were significantly enriched in different ontologies, indicating that single nucleotide mutations and base insertion and deletion mutation occurred in different gene ontologies in one pair of near isogenic lines (NILs)
Summary
In addition to producing nature fiber for the textile industry, cotton provides a large quantity of cottonseeds containing high-quality protein and oil[1]. Some gossypol biosynthesis genes have been characterized and used to reduce the gossypol content in cottonseeds[2,4,5]. Previous research has reported that the gossypol content is highly correlated with the number of pigment glands[18]. The gossypol content in cotton plants is closely related to the genetic types of pigment glands in cotton cultivars. Investigating the formation of pigment glands is meaningful for regulating the content of gossypol in cotton plants. The glandless cotton plant was thought to be mainly controlled by two recessive or one dominant gene. The resequencing of some specific cotton accessions could provide deeper insight into the genomic variations in upland cotton
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