Introgression of cotton leaf curl virus-resistant genes from Asiatic cotton (Gossypium arboreum) into upland cotton (G. hirsutum)

Categories of resistance in cotton genotypes, Gossypium spp. against cotton-melon aphid, Aphis gossypii (Hemiptera: Aphididae)

Cotton-melon aphid, Aphis gossypii Glover (Hemiptera: Aphididae), is emerging as a potential threat to cotton cultivation worldwide. The resistance categories in Gossypium arboreum to A. gossypii still need to be explored. We screened 87 G. arboreum and 20 Gossypium hirsutum genotypes against aphids under natural field conditions. Twenty-six selected genotypes from these 2 species were tested under glasshouse conditions for resistance categories (antixenosis, antibiosis, and tolerance). Resistance categories were assessed by no-choice antibiosis assay, free-choice aphid settling assay, cumulative aphid days using population buildup tests, chlorophyl loss index, and damage ratings. No-choice antibiosis experiment revealed that the G. arboreum genotypes GAM156, PA785, CNA1008, DSV1202, FDX235, AKA2009-6, DAS1032, DHH05-1, GAM532, and GAM216 had a significant adverse effect on aphid development time, longevity, and fecundity. Gossypium arboreum genotypes CISA111 and AKA2008-7 expressed a low level of antixenosis but possessed antibiosis and tolerance. Aphid resistance persisted uniformly at different plant developmental stages studied. The chlorophyl loss percentage and damage rating scores were lower in G. arboreum than in G. hirsutum genotypes, indicating the existence of tolerance in G. arboreum to aphids. Logical relations analysis of resistance contributing factors depicted the presence of antixenosis, antibiosis, and tolerance in the G. arboreum genotypes PA785, CNA1008, DSV1202, and FDX235, indicating their utility for evaluating the mechanisms of resistance and aphid resistance introgression breeding into G. hirsutum to develop commercially cultivated cotton lines.

Identification of Introgressed Alleles Conferring High Fiber Quality Derived From Gossypium barbadense L. in Secondary Mapping Populations of G. hirsutum L

The improvement of fiber quality is an essential goal in cotton breeding. In our previous studies, several quantitative trait loci (QTLs) contributing to improved fiber quality were identified in different introgressed chromosomal regions from Sea Island cotton (Gossypium barbadense L.) in a primary introgression population (Pop. A) of upland cotton (G. hirsutum L.). In the present study, to finely map introgressed major QTLs and accurately dissect the genetic contribution of the target introgressed chromosomal segments, we backcrossed two selected recombinant inbred lines (RILs) that presented desirable high fiber quality with their high lint-yielding recurrent parent to ultimately develop two secondary mapping populations (Pop. B and Pop. C). Totals of 20 and 27 QTLs for fiber quality were detected in Pop. B and Pop. C, respectively, including four and five for fiber length, four and eight for fiber micronaire, two and four for fiber uniformity, five and four for fiber elongation, and six and four for fiber strength, respectively. Two QTLs for lint percentage were detected only in Pop. C. In addition, seven stable QTLs were identified, including two for both fiber length and fiber strength and three for fiber elongation. Five QTL clusters for fiber quality were identified in the introgressed chromosomal regions, and negative effects of these chromosomal regions on lint percentage (a major lint yield parameter) were not observed. Candidate genes with a QTL-cluster associated with fiber strength and fiber length in the introgressed region of Chr.7 were further identified. The results may be helpful for revealing the genetic basis of superior fiber quality contributed by introgressed alleles from G. barbadense. Possible strategies involving marker-assisted selection (MAS) for simultaneously improving upland cotton fiber quality and lint yield in breeding programs was also discussed.

Identification and Characterization of miRNA Transcriptome in Asiatic Cotton (Gossypium arboreum) Using High Throughput Sequencing

MicroRNAs (miRNAs) are small 20-24nt molecules that have been well studied over the past decade due to their important regulatory roles in different cellular processes. The mature sequences are more conserved across vast phylogenetic scales than their precursors and some are conserved within entire kingdoms, hence, their loci and function can be predicted by homology searches. Different studies have been performed to elucidate miRNAs using de novo prediction methods but due to complex regulatory mechanisms or false positive in silico predictions, not all of them express in reality and sometimes computationally predicted mature transcripts differ from the actual expressed ones. With the availability of a complete genome sequence of Gossypium arboreum, it is important to annotate the genome for both coding and non-coding regions using high confidence transcript evidence, for this cotton species that is highly resistant to various biotic and abiotic stresses. Here we have analyzed the small RNA transcriptome of G. arboreum leaves and provided genome annotation of miRNAs with evidence from miRNA/miRNA∗ transcripts. A total of 446 miRNAs clustered into 224 miRNA families were found, among which 48 families are conserved in other plants and 176 are novel. Four short RNA libraries were used to shortlist best predictions based on high reads per million. The size, origin, copy numbers and transcript depth of all miRNAs along with their isoforms and targets has been reported. The highest gene copy number was observed for gar-miR7504 followed by gar-miR166, gar-miR8771, gar-miR156, and gar-miR7484. Altogether, 1274 target genes were found in G. arboreum that are enriched for 216 KEGG pathways. The resultant genomic annotations are provided in UCSC, BED format.

Genetic diversity analysis of Gossypium arboreum germplasm accessions using genotyping-by-sequencing

The diploid cotton species Gossypium arboreum possesses many favorable agronomic traits such as drought tolerance and disease resistance, which can be utilized in the development of improved upland cotton cultivars. The USDA National Plant Germplasm System maintains more than 1600 G. arboreum accessions. Little information is available on the genetic diversity of the collection thereby limiting the utilization of this cotton species. The genetic diversity and population structure of the G. arboreum germplasm collection were assessed by genotyping-by-sequencing of 375 accessions. Using genome-wide single nucleotide polymorphism sequence data, two major clusters were inferred with 302 accessions in Cluster 1, 64 accessions in Cluster 2, and nine accessions unassigned due to their nearly equal membership to each cluster. These two clusters were further evaluated independently resulting in the identification of two sub-clusters for the 302 Cluster 1 accessions and three sub-clusters for the 64 Cluster 2 accessions. Low to moderate genetic diversity between clusters and sub-clusters were observed indicating a narrow genetic base. Cluster 2 accessions were more genetically diverse and the majority of the accessions in this cluster were landraces. In contrast, Cluster 1 is composed of varieties or breeding lines more recently added to the collection. The majority of the accessions had kinship values ranging from 0.6 to 0.8. Eight pairs of accessions were identified as potential redundancies due to their high kinship relatedness. The genetic diversity and genotype data from this study are essential to enhance germplasm utilization to identify genetically diverse accessions for the detection of quantitative trait loci associated with important traits that would benefit upland cotton improvement.

CRISPR/Cas9: A Tool to Circumscribe Cotton Leaf Curl Disease

The begomoviruses (family Geminiviridae) associated with cotton leaf curl disease (CLCuD) pose a major threat to cotton productivity in South-East Asia including Pakistan and India. These viruses have single-stranded, circular DNA genome, of ∼2800 nt in size, encapsidated in twinned icosa-hedera, transmitted by ubiquitous whitefly and are associated with satellite molecules referred to as alpha- and betasatellite. To circumvent the proliferation of these viruses numerous techniques, ranging from conventional breeding to molecular approaches have been applied. Such devised strategies worked perfectly well for a short time period and then viruses relapse due to various reasons including multiple infections, where related viruses synergistically interact with each other, virus proliferation and evolution. Another shortcoming is, until now, that all molecular biology approaches are devised to control only helper begomoviruses but not to control associated satellites. Despite the fact that satellites could add various functions to helper begomoviruses, they remain ignored. Such conditions necessitate a very comprehensive technique that can offer best controlling strategy not only against helper begomoviruses but also their associated DNA-satellites. In the current scenario clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR associated nuclease 9 (Cas9) has proved to be versatile technique that has very recently been deployed successfully to control different geminiviruses. The CRISPR/Cas9 system has been proved to be a comprehensive technique to control different geminiviruses, however, like previously used techniques, only a single virus is targeted and hitherto it has not been deployed to control begomovirus complexes associated with DNA-satellites. Here in this article, we proposed an inimitable, unique, and broad spectrum controlling method based on multiplexed CRISPR/Cas9 system where a cassette of sgRNA is designed to target not only the whole CLCuD-associated begomovirus complex but also the associated satellite molecules.

Evaluation of cotton leaf curl virus resistance in BC1, BC2, and BC3 progenies from an interspecific cross between Gossypium arboreum and Gossypium hirsutum

Cotton leaf curl virus disease (CLCuD) is an important constraint to cotton production. The resistance of G. arboreum to this devastating disease is well documented. In the present investigation, we explored the possibility of transferring genes for resistance to CLCuD from G. arboreum (2n = 26) cv 15-Mollisoni into G. hirsutum (2n = 52) cv CRSM-38 through conventional breeding. We investigated the cytology of the BC₁ to BC₃ progenies of direct and reciprocal crosses of G. arboreum and G. hirsutum and evaluated their resistance to CLCuD. The F₁ progenies were completely resistant to this disease, while a decrease in resistance was observed in all backcross generations. As backcrossing progressed, the disease incidence increased in BC₁ (1.7–2.0%), BC₂ (1.8–4.0%), and BC₃ (4.2–7.0%). However, the disease incidence was much lower than that of the check variety CIM-496, with a CLCuD incidence of 96%. Additionally, the disease incidence percentage was lower in the direct cross 2(G. arboreum)×G. hirsutum than in that of G. hirsutum×G. arboreum. Phenotypic resemblance of BC₁ ∼BC₃ progenies to G. arboreum confirmed the success of cross between the two species. Cytological studies of CLCuD-resistant plants revealed that the frequency of univalents and multivalents was high in BC₁, with sterile or partially fertile plants, but low in BC₂ (in both combinations), with shy bearing plants. In BC₃, most of the plants exhibited normal bearing ability due to the high frequency of chromosome associations (bivalents). The assessment of CLCuD through grafting showed that the BC₁ to BC₃ progenies were highly resistant to this disease. Thus, this study successfully demonstrates the possibility of introgressing CLCuD resistance genes from G. arboreum to G. hirsutum.