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Key Message: Different kinship and resistance to cotton leaf curl disease (CLCuD) and heat were found between upland cotton cultivars from China and Pakistan. 175 SNPs and 82 InDels loci related to yield, fiber quality, CLCuD, and heat resistance were identified. Elite alleles found in Pakistani accessions aided local adaptation to climatic condition of two countries. Adaptation of upland cotton (Gossypium hirsutum) beyond its center of origin is expected to be driven by tailoring of the genome and genes to enhance yield and quality in new ecological niches. Here, resequencing of 456 upland cotton accessions revealed two distinct kinships according to the associated country. Fiber quality and lint percentage were consistent across kinships, but resistance to cotton leaf curl disease (CLCuD) and heat was distinctly exhibited by accessions from Pakistan, illustrating highly local adaption. A total of 175 SNP and 82 InDel loci related to yield, fiber quality, CLCuD and heat resistance were identified; among them, only two overlapped between Pakistani and Chinese accessions underscoring the divergent domestication and improvement targets in each country. Loci associated with resistance alleles to leaf curl disease and high temperature were largely found in Pakistani accessions to counter these stresses prevalent in Pakistan. These results revealed that breeding activities led to the accumulation of unique alleles and helped upland cotton become adapted to the respective climatic conditions, which will contribute to elucidating the genetic mechanisms that underlie resilience traits and help develop climate-resilient cotton cultivars for use worldwide., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Allotetraploid cotton is an economically important natural-fiber-producing crop worldwide. After polyploidization, Gossypium hirsutum L. evolved to produce a higher fiber yield and to better survive harsh environments than Gossypium barbadense, which produces superior-quality fibers. The global genetic and molecular bases for these interspecies divergences were unknown. Here we report high-quality de novo-assembled genomes for these two cultivated allotetraploid species with pronounced improvement in repetitive-DNA-enriched centromeric regions. Whole-genome comparative analyses revealed that species-specific alterations in gene expression, structural variations and expanded gene families were responsible for speciation and the evolutionary history of these species. These findings help to elucidate the evolution of cotton genomes and their domestication history. The information generated not only should enable breeders to improve fiber quality and resilience to ever-changing environmental conditions but also can be translated to other crops for better understanding of their domestication history and use in improvement.

Summary: Verticillium dahliae, one of the most destructive fungal pathogens of several crops, challenges the sustainability of cotton productivity worldwide because very few widely‐cultivated Upland cotton varieties are resistant to Verticillium wilt (VW). Here, we report that REVEILLE2 (RVE2), the Myb‐like transcription factor, confers the novel function in resistance to VW by regulating the jasmonic acid (JA) pathway in cotton. RVE2 expression was essentially required for the activation of JA‐mediated disease‐resistance response. RVE2 physically interacted with TPL/TPRs and disturbed JAZ proteins to recruit TPL and TPR1 in NINJA‐dependent manner, which regulated JA response by relieving inhibited‐MYC2 activity. The MYC2 then bound to RVE2 promoter for the activation of its transcription, forming feedback loop. Interestingly, a unique truncated RVE2 widely existing in D‐subgenome (GhRVE2D) of natural Upland cotton represses the ability of the MYC2 to activate GhRVE2A promoter but not GausRVE2 or GbRVE2. The result could partially explain why Gossypium barbadense popularly shows higher resistance than Gossypium hirsutum. Furthermore, disturbing the JA‐signalling pathway resulted into the loss of RVE2‐mediated disease‐resistance in various plants (Arabidopsis, tobacco and cotton). RVE2 overexpression significantly enhanced the resistance to VW. Collectively, we conclude that RVE2, a new regulatory factor, plays a pivotal role in fine‐tuning JA‐signalling, which would improve our understanding the mechanisms underlying the resistance to VW. [ABSTRACT FROM AUTHOR]

To the extent of our knowledge, applications of DNA markers in marker-assisted breeding of cotton are handicapped due to low genetic diversity in cotton germplasm. Cotton leaf curl disease, a disease of viral origin, has substantially depressed cotton production in Pakistan, and this disease is also an emerging threat to the neighboring cotton-growing countries like China and India. The present study was designed to identify DNA markers, predominately simple sequence repeats (SSRs), associated with tolerance and/or resistance to the disease. Based upon 2 years of disease-screening field experiments, a total of 10 cotton genotypes (five highly tolerant, four highly susceptible, and one immune) of diverse origin were selected from the available cotton germplasm (~1200 accessions) of the National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan. In total, 322 SSRs derived from bacterial artificial chromosome end sequences of Gossypium raimondii (one of the progenitor species of cultivated tetraploid cotton) were screened. Out of these, 65 primer pairs were found polymorphic, and the extent of genetic similarity was in the range of 81.7% to 98.7%. A similarity matrix was used for studying their phylogenetic relationship using unweighted pair-group method with arithmetic means (UPGMA) analysis. The dendrogram showed the grouping of the genotypes into two distinct clusters comprising tolerant and susceptible genotypes, respectively. Out of the polymorphic markers, two SSR markers, PR-91 and CM-43, that were amplified only in tolerant genotypes showed significant association with resistance to the disease. These preliminary results set the stage for initiating in-depth marker-trait association studies, which will be instrumental for initiating marker-assisted breeding in cotton. [ABSTRACT FROM AUTHOR]

Microsatellite regions in DNA fragments of Gossypium arboreum were explored and PCR products 500-800 bp long were analyzed for genomic simple sequence repeats (gSSRs). From 39 segments, 23 short gSSRs were identified; on average they occurred every 1.6 kb. Primers were used to amplify fragments from 18 diploid species representing 6 diploid genomes and 1 tetraploid species, G. hirsutum (AD). The phylogeny of diploid genomes was subsequently determined. No primer amplified the DNA from all genotypes; however, amplification occurred in 59% of 437 PCR events. All genomes were grouped into 2 clusters (a and b). The obtained phylogeny of the species parallels previous reports. The strategy adopted here is an efficient method of identifying new gSSRs from species not extensively explored. [ABSTRACT FROM AUTHOR]