Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement

Abstract

Cotton (Gossypium spp.) is the most important natural fiber crop worldwide. The diversity of Gossypium species also provides an ideal model for investigating evolution and domestication of polyploids. However, the huge and complex cotton genome hinders genomic research. Technical advances in high-throughput sequencing and bioinformatics analysis have now largely overcome these obstacles, bringing about a new era of cotton genomics. Here, we review recent progress in Gossypium genomics based on whole genome sequencing, resequencing, and comparative genomics, which have provided insights about the genomic basis of fiber biogenesis and the landscape of cotton functional genomics. We address current challenges and present multidisciplinary genomics-enabled breeding strategies covering the breadth of high fiber yield, quality, and environmental resilience for future cotton breeding programs. Gossypium Genomics at a Glance As the world's most important fiber crop and a major source of seed oil and protein, cotton is cultivated in more than 75 countries around the globe [1]. Cotton fibers are seed trichomes, up to 65 mm long, composed of almost pure cellulose, and provide a unique single-celled model system for studying cell elongation and cell wall biogenesis [2]. The Gossypium genus is extraordinarily diverse, with eight diploid genome groups (A-G, and K) and one allopolyploid group (AD) [3,4]. Hybridization and polyploidization of two parental diploids, an A genome-like species with a D genome-like species, has resulted in at least seven allotetraploid species. Two allotetraploid species, Gossypium hirsutum and Gossypium barbadense, evolved independently; these two account for over 90% of annual commercial fiber production. Gossypium is ideal for investigating the origin, evolution, and domestication of polyploids [5-7]. Highlights Cotton is an important natural fiber crop cultivated worldwide that also provides an ideal model for investigating evolution and domestication of polyploids Combinations of the latest technologies, such as optical mapping, high-throughput chromosome conformation capture (Hi-C), and Pacific Biosciences (PacBio) long-reads, have been used to generate multiple high-quality reference genomes of diploid and allotetraploid cotton. Comparative population genomics illuminated the genetic history of cotton domestication and identified the genomic variation determining fiber yield, quality, and stress resistance.

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

“…For example, line R28 carried the heterozygous fragment covering almost the entire chromosome A08, and line R126 carried a wide range of heterozygous fragments on different chromosomes which may result in colorful phenotype of the fuzz fiber (Additional file 7: Figure S1). Consistent with the previous reports [46,47], we speculate that this may be related to the interspecific segregation distortion.…”

Unravelling cotton RNAseq repositories to the fiber development specific modules and their alliance with the fiber-related traits

“…Cotton genome was refined over the year by different independent groups to get the well-annotated genes and unravel the evolution dynamics for fiber-specific features (Yang et al, 2020). Additionally, to understand the molecular and biological functions of genes involved in cotton fiber growth and development, the multi-omics approach was also taken into consideration (Pang et al, 2009; Rai et al, 2013; Song et al, 2015; Zou et al, 2016; Song et al, 2017; Kumar et al, 2018; Ayubov et al, 2019; Li et al, 2019).…”

Application of Genomics and Phenomics in Plant Breeding for Climate Resilience

“…ADSTs allows breeders and bioinformaticians to conduct genomic sequence comparisons for the identification and characterization of functional genomic regions. The comparisons of resequenced data against standardized reference genomes allow for the detection of existing haplotype and allelic diversity across genotypes [27]. The existing genetic or allelic diversity is an integral component of breeding programmes targeting various traits including climate resilience.…”