Structural Genomics

A recombinant inbred line (RIL) population derived from an intraspecific cross between two elite upland cotton cultivars, 0–153 with excellent fiber quanlity and sGK9708 as commercial variety. A genetic map which covered the whole genome of upland cotton was constructed by three types of markers (SLAF-SNP markers, chip-SNP makers and SSR markers). The consensus genetic map harbored 8295 markers included 5521 SLAF SNP markers, 2398 chip –SNP markers and 733 SSR markers). The total distance of genetic map were 5197.17cM and the avenge distance between adjust markers was 0.88 cM. Combined the 22 phenotype data of the RIL population and the genetic map, the QTLs for fiber quality traits (fiber strength, fiber length and micronaire) and yield traits (boll weight, lint percentage and seed index) were identified. The results showed that there were total of 177 QTLs for fiber length, 156 for fiber strength, 201 for micronaire, 253 for boll weight, 179 for lint percentage and 187 for seed index. Among them, 44 for fiber length, 39 for fiber strength, 42 for micronaire, 58 for boll weight, 35 for lint percentage and 38 for seed index were the stable ones which could be detected in at least three environments. And there were 32 QTLs cluster related to fiber length, 29 related to fiber strength, 18 related to micronaire, 30 related to boll weight, 18 related to lint percentage and 29 related to seed index. And there were 18 negtive related QTLs cluster for fiber length, 14 for fiber strength,11 for micronaire, 14 for boll weight, 18 for lint percentage and 12 for seed index.There were also eight QTL clusters between fiber strength and lint percentage and nine QTL clusters between fiber length and lint percentage, all the QTL clusters showed the different additive effect direction for the related traits, which was in accordance with the significant negative genetic corelation between the fiber quality and lint percentage. The QTL cluster of qCluster-chr7-1 could increase fiber length, fiber strength and seed index the qCluster-chr25-1 could increase the fiber length and fiber strength and reduce the lint percentage and boll weight. The further research including function of genes located on the QTL clusters and the interaction between these genes,which would lay foundations for improving the cotton fiber quality and yield simultaneously. Key words: upland cotton; fiber quality, High-density Genetic Map, QTL，RIL population Youlu Yuan as Corresponding authors

Verticillium wilt is one of the most destructive diseases affecting global cotton production. The development of Verticillium wilt resistant cultivars is one way to control the disease. Several studies have demonstrated that there existed Verticillium wilt resistant identify quantitative trait loci (QTL) on Dt_chr9 and its homologous chromosome At_chr9. In this study we combined the QTL detection power of genetic linkage mapping with the high resolution power of association mapping study to precisely dissect QTL controlling Verticillium wilt resistance on Dt_chr9 and At_chr9. 237 F2 lines from a cross between Zhongzhimian 2 (a cotton variety with superior resistance) and a sensitive variety, Jimian 11 were used to identify QTL for Verticillium wilt resistance with 72 SSRs randomly distributed on Dt_chr9 and At_chr9. At the same time, 120 lines from the China Elite Cotton germplasm collection were used to identify loci associated with Verticillium wilt resistance with more than 6000 SNPs distributed on Dt_chr9 and At_chr9, by using a regional association analysis-based fine-mapping strategy. We identified four Verticillium wilt resistance QTL on chromosome Dt_chr9 and At_chr9, among which one QTL, qVW- At_chr9-1 was validated by association mapping. Interestingly, this validated QTL explained 24.49% phenotype variation with a LOD value of 13.78, and located outside of the previously reported QTL regions on At_chr9 chromosome, implying a new major QTL detection. Linkage mapping defined the confidence interval of qVW- At_chr9-1 within 49539236 bp - 50898755 bp on At_chr9, while association mapping further narrowed down the confidence interval of qVW- At_chr9-1 within 49993040 bp - 50208544 bp on At_chr9, a region of 215.5 kb ( about 0.54cM). It is concluded that the application of Linkage mapping combined with association analysis enabled us to dramatically increase the resolution within the confidence interval of Verticillium wilt resistance QTL by-passing labor- and time-intensive fine mapping and accelerate the pace of QTL mapping projects.

Wild species of Gossypium present an impressive range of variation in many characters, all of which can potentially be exploited in cotton improvement programs. G. anomalum possesses several desirable characters such as extremely fine fibers, immunity to black arm and bacterial blight disease and tolerance to water deficit, as this species is endemic to relatively dry areas. To effectively introgression desirable traits into cultivated cotton from G. anomalum, we made crosses between G. hirsutum (A1A1D1D1) and G. anomalum (B1B1) and obtained triploid hybrids with the genome composition A1D1Bl. Then we treated triploid hybrids with 0.15% colchicine and obtained a putative fertile hexaploid (A1A1D1D1B1B1) in order to resolve interspecific hybrid sterility problems. We demonstrated the hybridity and doubled status of a (G. anomalum × G. hirsutum)2 hexaploid using morphological, cytological and molecular marker methods. To effectively monitor G. anomalum genome components in the G. hirsutum background, we developed 5974 non-redundant G. anomalum derived SSR primer pairs using RNA-Seq technology, which were combined with a publicly available physical map. Based on this combined map and segregation data from the BC2F1 population, we identified a set of 230 informative G. anomalum-specific SSR markers distributed on the chromosomes, which cover 95.72 % of the cotton genome. After analyzing BC2F1 segregation data, 50 recombination types from 357 recombination events were identified, which cover 81.48 % of the corresponding G. anomalum genome. A total of 203 recombination events occurred on chromosome 11, accounting for 56.86 % of the recombination events on all chromosomes. By successive backcrosses and selfing combined with marker assisted selection, about 60 chromosome segment substitution lines (CSSLs) were developed. Genomic regions that affect fiber quality, plant height and boll size were identified. This study represents an important step towards introgressing desirable traits into cultivated cotton from the wild cotton species G. anomalum.

Upland cotton (Gossypium hirsutum) dominates the production of most-utilized natural textile fibre crop and contributes 95 per cent of the world’s cotton production but, it's fibre qualities are less superior than G. barbadense and this is the only best genetic resource among cultivated species for improving fibre quality traits of upland cotton. Higher the counts of the yarn, finer is the garment. G. hirsutum cotton produces 30-50's counts yarn whereas, G. barbadense is known for superior quality fibre, produces 60-120's counts yarn. Identification of more number of molecular markers in G. barbadense is very much necessary to construct a high-density linkage map/fine gene map/QTL map, which will ease the precise introgression of fibre QTLs in to upland cotton. The present study explored the feasibility of identifying single nucleotide polymorphism (SNP) markers between Suvin (known as Jewel in the Indian cotton crown for fiber quality) and BCS23-18-7 (known for high-yielding and early maturity) genotypes of G. barbadense cotton through whole genome re-sequencing. After filtering out poor quality reads, a total of 1,176,543,126 and 1,301,334,450 reads were obtained from Suvin and BCS23-18-7 respectively. By aligning the sequences with reference genomes, they recorded highest alignment with G. barbadense reference genome (97.44 & 95.27 % respectively) followed by G. hirsutum (95.03 & 93.03 % respectively), G. arboreum (78.29 & 77.05 % respectively), G. raimondii (95.16 & 54.47 % respectively). The highest number of 12,276,464 SNPs (10,110,752 homozygous) and Indels (1,248,940) were observed between Suvin and BCS23-18-7 when G. hirstum used as a reference genome. Whereas, 2,604,107 SNPs (1,020,162 homozygous) and Indels (592,364) were observed with reference genome G. barbadense. The total size of 1.98 Gb and 1.99 Gb scaffold assembly with the coverage of 77 and 77.6 percent of G. barbadense genome was constructed from Suvin and BCS23-18-7 respectively. Based on gene annotation for these polymorphic SNPs through reference genome, 20K SNPs responsible for fiber, abiotic and biotic stress related traits were considered for inclusion in SNP chip preparation. These SNP chip will be used for genotyping. Keywords: QTL, SNP, Assembly, Reference and Aligning

Background: Fusarium wilt and Verticillium wilt of cotton are two important diseases adversely affecting cotton yield in China. Thus, disease-resistant cultivars are urgently needed to ensure stable cotton production. In this study, Ekangmian 9 and six other cotton varieties resistant to Fusarium wilt and differentially resistant or tolerant to Verticillium wilt were used as parents in diallel crosses. The main agronomic and fiber quality traits of the offspring were studied regarding genetic variance components, genetic effects, correlations, and competitive advantages. This study may be relevant for enhancing the selection of parents for hybridizations and for improving the selection of offspring and the application of heterosis. Results: Most of the examined traits were controlled by additive genetic effects. Additionally, P2 (Ekangmian 9 or Jing 55173), P5 (CCRI 23), and P6 (Shiyuan 321) were useful for improving the yield traits of their offspring. Moreover, P2 also significantly decreased the incidence of Verticillium wilt, while not adversely affecting fiber quality traits. The P1 × P2, P2 × P5, and P4 × P6 combinations were associated with mid-parent heterosis and competitive advantages. Correlation analyses revealed that increases in lint yield were mainly related to decreases in the diseased plant rate and infection index during the flowering period as well as increases in seed cotton yield. Conclusion: Of the analyzed cotton varieties, P2 (Ekangmian 9 or Jing 55173) may be the most appropriate parent for improving offspring characteristics, especially yield traits. In this study, P2 was included in four superior combinations (i.e., P1 × P2, P2 × P5, P2 × P4, and P2 × P6). Furthermore, Ekangmian 9 has been used as a parent in hybridizations that have resulted in a series of new high-yielding and high-quality cotton varieties including CCRI63 and CCRI66. Key words: Ekangmian 9, Breeding of Verticillium wilt-resistant cultivars, Diallel analysis, Genetic effects, Heterosis, Correlation analysis