Figure 5 - available via license: Creative Commons Attribution-NonCommercial 4.0 International
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Schematic drawing that illustrates the evolution of most chromosomes. This figure is available in black and white in print and in colour at DNA Research online.
Source publication
A high-density linkage map was constructed using 1,885 newly obtained loci and 3,747 previously published loci, which included
5,152 loci with 4696.03 cM in total length and 0.91 cM in mean distance. Homology analysis in the cotton genome further confirmed
the 13 expected homologous chromosome pairs and revealed an obvious inversion on Chr10 or Chr...
Citations
... Previous researchers revealed numerous qualitative trait loci (QTLs) related to FS by employing linkage analysis or genome-wide association study using various markers such as amplified fragment length polymorphisms, restriction fragment length polymorphisms, and simple sequence repeats (SSRs) on samples from different populations (Fang et al., 2017;Ning et al., 2014). With the refinement of cotton reference genome sequencing (Li et al., 2015;Zhang et al., 2015;Hu et al., 2019;Wang et al., 2019;Ma et al., 2021), high-density single-nucleotide polymorphisms (SNPs), individually and in conjunction with SSRs and other markers, were used to identify several FS-related genes (Islam et al., 2016;Li et al., 2016;Sun et al., 2017;Zhang et al., 2017;Ma et al., 2018;Feng et al., 2020;He et al., 2021;Yang et al., 2022). For example, Ma et al. (2018) conducted a re-sequencing study on 419 core germplasm resources and detected 630 FS-related SNPs. ...
High fiber strength (FS) premium cotton has significant market demand. Consequently, enhancing FS is a major objective in breeding quality cotton. However, there is a notable lack of known functionally applicable genes that can be targeted for breeding. To address this issue, our study used specific length–amplified fragment sequencing combined with bulk segregant analysis to study FS trait in an F2 population. Subsequently, we integrated these results with previous quantitative trait locus mapping results regarding fiber quality, which used simple sequence repeat markers in F2, F2:3, and recombinant inbred line populations. We identified a stable quantitative trait locus qFSA06 associated with FS located on chromosome A06 (90.74–90.83 Mb). Within this interval, we cloned a gene, GhALDH7B4_A06, which harbored a critical mutation site in coding sequences that is distinct in the two parents of the tested cotton line. In the paternal parent Ji228, the gene is normal and referred to as GhALDH7B4_A06O ; however, there is a nonsense mutation in the maternal parent Ji567 that results in premature termination of protein translation, and this gene is designated as truncated GhALDH7B4_A06S . Validation using recombinant inbred lines and gene expression analysis revealed that this mutation site is correlated with cotton FS. Virus-induced gene silencing of GhALDH7B4 in cotton caused significant decreases in FS and fiber micronaire. Conversely, GhALDH7B4_A06O overexpression in Arabidopsis boosted cell wall component contents in the stem. The findings of our study provide a candidate gene for improving cotton fiber quality through molecular breeding.
... A region containing three or more QTLs (which can be used to control different traits) within 20 cM of the chromosome is called a QTL cluster. It is estimated that the average 1 cM of cotton genome is equivalent to the physical region of 0.5 Mb [45]. The distribution of six QTL clusters was also found in this study (Table 5, Figure 4), namely A02-cluster, A03-cluster, A04-cluster, D02-cluster, D07-cluster and D08-cluster. ...
As one of the most widely cultivated cotton species in China, upland cotton has moderate fiber quality and wide applicability, but its genetic basis is relatively narrow. To expand genetic diversity and improve fiber quality, in this study an introgression population (BC5S5) containing 107 lines was constructed by using G. hirsutum acc. 4105 as the recurrent parent and G. tomentosum as the donor parent. Using the specific-locus amplified fragment sequencing (SLAF-seq) strategy, 3157 high-throughput single nucleotide polymorphism (SNP) markers were obtained. Linkage analysis showed that a total of ninety-one QTLs related to fiber quality traits were detected in three environments, and the phenotypic variance explained (PVE) rates were 4.53–20.92%. Forty-six QTL (50.55%) synergistic genes were derived from G. tomentosum. Among them, qFS-A02-1 and qSCI-A02-1 were stably detected with a PVE of 9.8–16.71% and 14.78–20.92%, respectively. Within the candidate interval, Ghir_A02G012730, Ghir_A02G012790 and Ghir_A02G012830 were found to be possibly involved in cellulose and cell wall biosynthesis, with a relatively high expression during fiber development, 20 DPA and 25 DPA, which suggested that these three genes may be involved in the regulation of fiber strength traits, but their functions need further validation to determine the regulatory mechanism. Our research lays the foundation of fiber quality related to basic genetic research and breeding in cotton.
... All hindered by limited ultra-precision genetic mapping before the publishing of the complete genome sequences for four Gossypium species in 2013. The cotton plantation industry's access to fairly large cotton-genome linkage maps may enable gene mapping, high-throughput markers, cotton cloning and gene isolation [28,29]. In the previous 10 years, approx. ...
... All hindered by limited ultra-precision genetic mapping before the publishing of the complete genome sequences for four Gossypium species in 2013. The cotton plantation industry's access to fairly large cotton-genome linkage maps may enable gene mapping, high-throughput markers, cotton cloning and gene isolation [28,29]. In the previous 10 years, approx. ...
Gossypium spp. (Cotton) is the world’s most valuable natural fiber crop. Gossypium species’ variety makes them a good model for studying polyploid evolution and domestication. The past decade has seen a dramatic shift in the field of functional genomics from a theoretical idea to a well-established scientific discipline. Cotton functional genomics has the potential to expand our understanding of fundamental plant biology, allowing us to more effectively use genetic resources to enhance cotton fiber quality and yield, among with using genetic data to enhance germplasm. This chapter provides complete review of the latest techniques and resources for developing elite cotton genotypes and determining structure that have become accessible for developments in cotton functional genomics. Bioinformatics resources, including databases, software solutions and analytical tools, must be functionally understood in order to do this. Aside from GenBank and cotton specific databases like CottonGen, a wide range of tools for accessing and analyzing genetic and genomic information are also addressed. This chapter has addressed many forms of genetic and genomic data now accessible to the cotton community; fundamental bioinformatics sources related to cotton species; and with these techniques cotton researchers and scientists may use information to better understand cotton’s functions and structures.
... Cotton (Gossypium spp.) is an important cash crop species worldwide, providing an essential natural resource for the textile industry. Due to its high yield and wide adaptation, upland cotton (Gossypium hirsutum L.) accounts for more than 95% of global cotton production (Lacape et al., 2003;Li X. M. et al., 2016). However, extra-long staple, Pima, Egyptian, or Sea Island cotton (Gossypium barbadense L.) have excellent fiber quality with long, strong and fine fibers, but their low yield and requirements for warm and dry weather conditions limit their cultivation area Said J. I. et al., 2015). ...
Cotton is the most important fiber crop and provides indispensable natural fibers for the textile industry. Micronaire (MIC) is determined by fiber fineness and maturity and is an important component of fiber quality. Gossypium barbadense L. possesses long, strong and fine fibers, while upland cotton (Gossypium hirsutum L.) is high yielding with high MIC and widely cultivated worldwide. To identify quantitative trait loci (QTLs) and candidate genes for MIC in G. barbadense, a population of 250 backcross inbred lines (BILs), developed from an interspecific cross of upland cotton CRI36 × Egyptian cotton (G. barbadense) Hai7124, was evaluated in 9 replicated field tests. Based on a high-density genetic map with 7709 genotyping-by-sequencing (GBS)-based single-nucleotide polymorphism (SNP) markers, 25 MIC QTLs were identified, including 12 previously described QTLs and 13 new QTLs. Importantly, two stable MIC QTLs (qMIC-D03-2 on D03 and qMIC-D08-1 on D08) were identified. Of a total of 338 genes identified within the two QTL regions, eight candidate genes with differential expression between TM-1 and Hai7124 were identified. Our research provides valuable information for improving MIC in cotton breeding.
... Interestingly, in both maps, chromosome D 5 02 had a smaller map size but with the highest percentage of SD (Table 1). Similar results have been observed in other linkage maps in cotton (Yu et al. 2011;Li et al. 2016). ...
Background
Segregation distortion (SD) is a common phenomenon among stable or segregating populations, and the principle behind it still puzzles many researchers. The F 2:3 progenies developed from the wild cotton species of the D genomes were used to investigate the possible plant transcription factors within the segregation distortion regions (SDRs). A consensus map was developed between two maps from the four D genomes, map A derived from F 2:3 progenies of Gossypium klotzschianum and G. davidsonii while Map B from G. thurberi and G. trilobum F 2:3 generations. In each map, 188 individual plants were used.
Results
The consensus linkage map had 1 492 markers across the 13 linkage groups with a map size of 1 467.445 cM and an average marker distance of 1.037 0 cM. Chromosome D 5 02 had the highest percentage of SD with 58.6%, followed by Chromosome D 5 07 with 47.9%. Six thousand and thirty-eight genes were mined within the SDRs on chromosome D 5 02 and D 5 07 of the consensus map. Within chromosome D 5 02 and D 5 07, 2 308 and 3 730 genes were mined, respectively, and were found to belong to 1 117 gourp out of which 622 groups were common across the two chromosomes. Moreover, genes within the top 9 groups related to plant resistance genes (R genes), whereas 188 genes encoding protein kinase domain (PF00069) comprised the largest group. Further analysis of the dominant gene group revealed that 287 miRNAs were found to target various genes, such as the gra-miR398, gra-miR5207, miR164a, miR164b, miR164c among others, which have been found to target top-ranked stress-responsive transcription factors such as NAC genes. Moreover, some of the stress- responsive cis -regulatory elements were also detected. Furthermore, RNA profiling of the genes from the dominant family showed that higher numbers of genes were highly upregulated under salt and osmotic stress conditions, and also they were highly expressed at different stages of fiber development.
Conclusion
The results indicated the critical role of the SDRs in the evolution of the key regulatory genes in plants.
... For instance, several scaffolds belong to different chromosomes were present in one pseudo-molecule of G. arboreum. Several previous studies reported that draft sequenced genome of G. arboreum [27] contained errors and mis-assemblies [8,29,30], however this draft genome did not undergo precise quality improvement to correct errors. So, knowing how to assemble this genome accurately, how to best make use of the highly fragmented assemblies and how to perform these applications at the lowest cost are important in today's funding environment [31]. ...
Background:
Genome sequencing technologies have been improved at an exponential pace but precise chromosome-scale genome assembly still remains a great challenge. The draft genome of cultivated G. arboreum was sequenced and assembled with shotgun sequencing approach, however, it contains several misassemblies. To address this issue, we generated an improved reassembly of G. arboreum chromosome 12 using genetic mapping and reference-assisted approaches and evaluated this reconstruction by comparing with homologous chromosomes of G. raimondii and G. hirsutum.
Results:
In this study, we generated a high quality assembly of the 94.64 Mb length of G. arboreum chromosome 12 (A_A12) which comprised of 144 scaffolds and contained 3361 protein coding genes. Evaluation of results using syntenic and collinear analysis of reconstructed G. arboreum chromosome A_A12 with its homologous chromosomes of G. raimondii (D_D08) and G. hirsutum (AD_A12 and AD_D12) confirmed the significant improved quality of current reassembly as compared to previous one. We found major misassemblies in previously assembled chromosome 12 (A_Ca9) of G. arboreum particularly in anchoring and orienting of scaffolds into a pseudo-chromosome. Further, homologous chromosomes 12 of G. raimondii (D_D08) and G. arboreum (A_A12) contained almost equal number of transcription factor (TF) related genes, and showed good collinear relationship with each other. As well, a higher rate of gene loss was found in corresponding homologous chromosomes of tetraploid (AD_A12 and AD_D12) than diploid (A_A12 and D_D08) cotton, signifying that gene loss is likely a continuing process in chromosomal evolution of tetraploid cotton.
Conclusion:
This study offers a more accurate strategy to correct misassemblies in sequenced draft genomes of cotton which will provide further insights towards its genome organization.
... In cotton, genetic inversions have been roughly detected by high-density genetic linkage maps with simple sequence repeat (SSR) markers [16][17][18]. Presently, the next generation sequencing (NGS) method provides a promising and accurate approach to detect SVs. With the publication of the reference genomes of two diploid (G. ...
Structural variation is a major type of genetic variation that can potentially induce powerful genetic effects. In this study, we examined the Inv(A07)p1.09p2.23 genetic inversion in brown fibre cotton at the individual and population genetics levels. A dark-brown fibre mutant that resulted from a distant hybridization between Gossypium barbadense and G. hirsutum, and a natural population including 30 dark-brown, 70 light-brown and 21 white fibre cotton accessions were collected to perform a functional study of this micro-inversion. The results showed that Inv(A07)p1.09p2.23 can be detected by high-throughput resequencing method, and induce micro-deletion, gene disruption (Ghir_A07G000980) and abnormal gene expression in the breakpoint regions. Inv(A07)p1.09p2.23 existed in only dark-brown fibre cotton, had undergone negative selection in elite brown fibre cultivars, and was significantly associated with fibre colour and nine fibre traits. In the Inv(A07)p1.09p2.23 region, nucleotide diversity was lower, recombination was absent, and linkage disequilibrium was higher. Overall, this inversion event in dark-brown fibre cotton produced significant genetic effects, and this study will guide us to better understand the genetic effects of inversion events in dark-brown fibre cotton.
... When FITC detection and Texas Red detection were superimposed, three populations of chromosomes are differentiated for the HTL trispecies hybrid (Fig. 5B). Thirteen chromosomes appeared green and were those from G. longicalyx; thirteen large chromosomes appeared yellow-orange and were those from G. hirsutum Asubgenome, twenty six small chromosomes appeared red and were those from G. hirsutum D-subgenome and G. thurberi D1 genome since the D genome is comprised of the smallest chromosomes (Phillips and Strickland 1966;Konan et al. 2009;Li et al. 2016). For the Backcross-2 progenies, GISH revealed presence of entire chromosomes of G. longicalyx as well as recombinant chromosomes (Fig. 5D). ...
Wild cotton species are an important source of desirable genes for genetic improvement of cultivated cotton Gossypium hirsutum Linnaeus, 1763. For the success of such an improvement, chromosome pairings and recombinations in hybrids are fundamental. The wild African species G. longicalyx Hutchinson & Lee, 1958 could be used as donor of the desirable trait of fiber fineness. Twelve BC1 plants obtained from the backcrossing of [( G. hirsutum × G. thurberi Todaro, 1877) ² × G. longicalyx ] (A h D h D 1 F 1 , 2n = 4x = 52) trispecies hybrid (HTL) by G. hirsutum (cv. C2) (A h A h D h D h , 2n = 4x = 52) were investigated for meiotic behaviour and plant fertility. Their chromosome associations varied as follows: (2.5 to 11.5) I + (17 to 22) II + (0.31 to 1.93) III + (0.09 to 1.93) IV + (0 to 0.07) V + (0 to 0.14) VI. Their pollen fertility ranged from 4.67 to 32.10 %. Only four BC1 plants produced a few seeds through self-pollination. The remaining BC1 were totally self-sterile and usually presented the highest number of univalents. All BC1 materials produced BC2 seeds (0.44 to 6.50 seeds per backcross) with the number of seeds negatively correlated with the number of univalents (R ² = 0.45, P < 0.05). Most BC1 plants gave significantly finer fiber compared to the cultivated G. hirsutum . SSR markers showed a segregation of wild alleles among the backcross derivatives and Genomic in situ hybridization (GISH) revealed presence of entire chromosomes of G. longicalyx as well as recombinant chromosomes in the backcross derivatives. The significance and details of these results are presented and the prospects of successfully exploiting these plant materials are discussed.
... The Cas9 orthologue of CRISPR/Cas-system was obtained from Staphylococcus aureus (SaCas9) ( Steinert et al. 2015). The CRISPR/ Cas9-based system has been extensively used in plants to improve qualitative and quantitative traits and to confer resistance against various phytopathogens ( Li et al. 2016;Nekrasov et al. 2017;Steinert et al. 2015). In order to exploit the unique binding ability of Cas9 to any complementary sequence, Cas9 was engineered to abolish its endonuclease activity and resulted into catalytically inactive protein, called dead Cas9 or dCas9. ...
... After whole-genome cotton sequencing, the major challenge could be the functional annotations and empirical investigations of the genome biology. Unlike other crop and model plants, a few genetic linkage maps are available for cotton ( Li et al. 2016). Such genetic maps may provide a base for genetic marker development, gene mapping and effective characterization of different genes. ...
Cotton has a tremendous economic value worldwide due to its high-quality
fiber, edible oil and protein contents. However, the intensifying scenario of
human population expansion and global environmental changes demand a proportionate
increase in cotton production. In the past, several successful attempts have
been made by introgression of many quality- and yield-related traits into elite cotton
cultivars through conventional breeding. However, those measures are time consuming
due to the reliance on introgression of naturally-existing genetic variation
through extensive backcrossing. Nonetheless, plant breeding can be accelerated
through modern genome editing (GE) tools. Various GE techniques including zinc
finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs),
and clustered regularly interspaced palindromic repeats and CRISPR-associated
proteins systems (CRISPR/Cas)-based approaches have been successfully employed
for various crop plants. Among them, CRISPR/Cas-based approaches hold great GE
potential due to their simplicity, competency and versatility. In cotton, this system
can regulate the gene expression associated with quality traits, to circumscribe phytopathogens
and/or to stack molecular traits at a desired locus. In gene stacking
through site-specific endonucleases, the desired genes can be introduced in close
proximity to a specific locus in the cotton genome with a low risk of segregation.
However, such executions are tedious to achieve through classical breeding techniques.
Moreover, through the CRISPR/Cas-based approaches, transgene-free cotton
plants can easily be produced by selfing or backcrossing to meet the current genetically modified organisms (GMO) guidelines. In this chapter, we address the
potential application of CRISPR/Cas-based approaches in available whole cotton
genomes to sustain cotton productivity, and achieve genetic improvement, pathogen
resistance and agronomic traits. Future prospects of GE applications in cotton
breeding are also addressed.
