Collinearity analysis of allotetraploid Gossypium tomentosum and Gossypium darwinii.

Gossypium tomentosum and G. darwinii are wild allotetraploid cotton species, characterized by many excellent traits, including fiber fineness, drought tolerance, and Fusarium and Verticillium wilt resistance. Based on the construction of F2 linkage groups of G. hirsutum x G. tomentosum and G. hirsutum x G. darwinii, two genetic linkage maps were compared. As a result, we found a total of seven inverted fragments on chr02, chr05, chr08, chr12, chr14, chr16, and chr25, and three translocated fragments on chr05, chr14, and chr26. In addition, comparison of the inverted and translocated fragments revealed that the orientation of four of seven markers in G. tomentosum were consistent with G. hirsutum or G. raimondii. The orientation of one of seven inverted markers of G. darwinii was consistent with G. hirsutum, and the orientation of one of three translocated markers of G. tomentosum was consistent with G. raimondii. These results indicate that, in comparison to G. darwinii, G. tomentosum has a closer genetic relationship to G. hirsutum. These findings will be important for our understanding on the genome structure of G. tomentosum and G. darwinii, and set the scene for further in-depth genome research such as fine mapping, tagging genes of interest from wild relatives, and evolutionary study.

Mapping QTLs for drought tolerance in an F2:3 population from an inter-specific cross between Gossypium tomentosum and Gossypium hirsutum.

Cotton is one of the most important natural fiber crops in the world. Its growth and yield is greatly limited by drought. A quantitative trait locus (QTL) analysis was therefore conducted to investigate the genetic basis of drought tolerance in cotton (Gossypium spp) using 188 F2:3 lines developed from an inter-specific cross between a wild cotton species, G. tomentosum, and an upland cotton, G. hirsutum (CRI-12). A genetic map was constructed using 1295 simple sequence repeat markers, which amplified 1342 loci, distributed on 26 chromosomes, covering 3328.24 cM. A field experiment was conducted in two consecutive years (2014 and 2015) and 11 morphological and physiological traits were recorded under water-limited (W1)/well-watered (W2) regimes at three growth stages (bud, flowering, and full boll). The traits measured included chlorophyll content, plant height, leaf area, leaf number, leaf fresh weight, leaf dry weight, boll weight, number of bolls per plant, and the number of fruiting branches. Sixty-seven and 35 QTLs were found under the W1 and W2 conditions, respectively. Of these, the majority exhibited partial dominance or over-dominance genetic effects for increasing the trait values. Four consistent QTLs were found under the W1 treatment on chromosomes 5, 8, 9, and 16, whereas no consistent QTL was found in W2. Thirteen QTL clusters were also identified on nine chromosomes (2, 3, 5, 6, 9, 14, 15, 16, and 21). These results will help to elucidate the genetic basis of drought tolerance in cotton.

Construction and characterization of a bacterial artificial chromosome library for the allotetraploid Gossypium tomentosum.

Gossypium tomentosum is a wild allotetraploid species with the (AD)5 genome. It is characterized by many useful traits including finer fiber fineness, drought tolerance, and Fusarium and Verticillium resistance. We constructed the first bacterial artificial chromosome library for Gossypium tomentosum. With high quality and broad coverage, this library includes 200,832 clones, with an average insert size of about 122 kb and fewer than 3% empty clones. Our library is approximately 10-fold the size of the (AD)5-genome (2400 Mb) and provides a 99.7% probability of isolating genes of interest or their sequences. Seven of eight simple sequence repeats markers that are located on five different chromosomes and linked with resistance to Verticillium wilt could amplify the 50 superpools and obtained one to five hits. This high capacity library will be an important genomic resource for classifying and analyzing the evolution of allotetraploid cotton species as well as for isolating disease-resistance and drought-tolerance genes.

Genetic diversity and relationship analysis of Gossypium arboreum accessions.

Simple sequence repeat techniques were used to identify the genetic diversity of 101 Gossypium arboreum accessions collected from India, Vietnam, and the southwest of China (Guizhou, Guangxi, and Yunnan provinces). Twenty-six pairs of SSR primers produced a total of 103 polymorphic loci with an average of 3.96 polymorphic loci per primer. The average of the effective number of alleles, Nei's gene diversity, and Shannon's information index were 0.59, 0.2835, and 0.4361, respectively. The diversity varied among different geographic regions. The result of principal component analysis was consistent with that of unweighted pair group method with arithmetic mean clustering analysis. The 101 G. arboreum accessions were clustered into 2 groups.

Characterization and development of chloroplast microsatellite markers for Gossypium hirsutum, and cross-species amplification in other Gossypium species.

Cotton is an important economic crop worldwide; its fiber, commonly known as cotton lint, is the main natural source for the textile industry. Sixty chloroplast microsatellites were identified and characterized from the complete sequence of the Gossypium hirsutum chloroplast genome using a bioinformatic approach. Twenty chloroplast microsatellite loci were polymorphic in the 66 Gossypium germplasm accessions. A total of 85 alleles were detected, with allele numbers varying from 2-7 per locus. Polymorphism information content varied from 0.02-0.66, with a mean of 0.48. Additionally, transferability of the 20 polymorphic chloroplast microsatellite primers was evaluated in other 31 Gossypium species. Sixteen markers were successfully amplified across all species tested, while the remaining 4 markers cross-amplified in most species tested. These polymorphic chloroplast microsatellite markers may be useful tool for studies of individual identification, genetic diversity, evolution, conservation genetics, and molecular breeding in Gossypium.