Abstract
SummaryThe diploid wild cotton species Gossypium australe possesses excellent traits including resistance to disease and delayed gland morphogenesis, and has been successfully used for distant breeding programmes to incorporate disease resistance traits into domesticated cotton. Here, we sequenced the G. australe genome by integrating PacBio, Illumina short read, BioNano (DLS) and Hi‐C technologies, and acquired a high‐quality reference genome with a contig N50 of 1.83 Mb and a scaffold N50 of 143.60 Mb. We found that 73.5% of the G. australe genome is composed of various repeat sequences, differing from those of G. arboreum (85.39%), G. hirsutum (69.86%) and G. barbadense (69.83%). The G. australe genome showed closer collinear relationships with the genome of G. arboreum than G. raimondii and has undergone less extensive genome reorganization than the G. arboreum genome. Selection signature and transcriptomics analyses implicated multiple genes in disease resistance responses, including GauCCD7 and GauCBP1, and experiments revealed induction of both genes by Verticillium dahliae and by the plant hormones strigolactone (GR24), salicylic acid (SA) and methyl jasmonate (MeJA). Experiments using a Verticillium‐resistant domesticated G. barbadense cultivar confirmed that knockdown of the homologues of these genes caused a significant reduction in resistance against Verticillium dahliae. Moreover, knockdown of a newly identified gland‐associated gene GauGRAS1 caused a glandless phenotype in partial tissues using G. australe. The G. australe genome represents a valuable resource for cotton research and distant relative breeding as well as for understanding the evolutionary history of crop genomes.
Highlights
In modern agricultural ecosystem, the narrow genetic base of modern crop cultivars, in which diversity has been lost in domestication, is becoming a major bottleneck for crop improvement programmes, especially for cultivated cotton
Gossypium australe has shown excellent resistance to the fungus disease Verticillium wilt, and the disease had little influence on morphology of G. australe plants (Figure 1a,b); in contrast, the stems and leaves of G. arboreum cultivar plants were greatly damaged after infection with Verticillium wilt
Another prominent trait of G. australe is delayed gland morphogenesis, and the seeds of G. australe (Figure 1c,d,e) have no gland in seed, but were observed during seeds germinate process, differing from that in G. arboretum, which is glanded in whole plants (Figure 1f,g,h)
Summary
The narrow genetic base of modern crop cultivars, in which diversity has been lost in domestication, is becoming a major bottleneck for crop improvement programmes, especially for cultivated cotton. Genomic analyses of CWRs generate data that support the use of CWRs to expand the genetic diversity of crop plants, which will strongly promote biodiversity, agricultural sustainability and food security (Brozynska et al, 2016). It is becoming increasingly important for genomic studies on CWRs; many such reports published in 2018 and 2019 (Arora et al, 2019; Milner et al, 2019), including wild rice (Zhao et al, 2018), wild wheat (Thind et al, 2018), soya bean wild relatives (Xie et al, 2019), wild tomato (Schmidt et al, 2017), wild peanut (Yin et al, 2018) and so on.
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