Displaying 31 - 40 of 60

Inducement and identification of chromosome introgression and translocation of Gossypium australe on Gossypium hirsutum

Germplasm and Genetic Stocks
Authors: 
Wang, Yingying
Zhou, Baoliang
Abstract: 
G. hirsutum-G. australe chromosome exchanges were very limited, impeding the stable transference of useful genes from G. australe (G2G2 genome) into the most cultivated cotton, G. hirsutum (AADD). In the present report, the pollen from a pentaploid (2n=AADDG2) of G. hirsutum-G. australe was irradiated with seven different doses ranging from 10 to 40 Grays and used to pollinate emasculated flowers of G. hirsutum over three consecutive years. Our results indicated that irradiation greatly increased the genetic recombination rates of the G. hirsutum and G. australe chromosomes and a total of 107 chromosome introgression individuals in 192 GISH-negative (with no GISH signal on chromosome) survived individuals, 11 chromosome translocation individuals (containing 12 chromosome translocation events) and 67 chromosome addition individuals were obtained in 70 GISH-positive (with GISH signal(s) on chromosome(s)) survived individuals, which are invaluable for mining desirable genes from G. australe. Multicolor genomic in situ hybridization results showed that there were three types of translocation, whole arm translocation, large alien segment translocation and small alien segment translocation, and that all translocations occurred between the G2-genome and the A-subgenome chromosomes in G. hirsutum. We also found that higher doses induced much higher rates of chromosome variation but also greatly lowered the seed viability and seedling survivability. Therefore, we concluded that irradiation can be used to induce chromosome introgressions and chromosome translocations and promote chromosome exchanges between cultivated and wild species. In addition, by balancing the rates of chromosome introgression and translocation to those of seed set, seed germination, and seedling rates in the M1 generation, we suppose that the dosage of 20 Grays is the most suitable. The established methodology may guide the utilization of the tertiary gene pool of Gossypium species such as G. australe in cotton breeding in the future.

Introgression leads to genetic divergence for maturity and fiber quality in upland cotton

Germplasm and Genetic Stocks
Authors: 
Du, Xiongming
He,ShouPu
Sun, Gaofei
Wang, Pengpeng
Jia, Yinhua
Pan, Zhaoe
Gong, Wenfang
Abstract: 
Understanding the genetic diversity and genetic divergence in population structure of germplasms is important when selecting parents for crop breeding. The genomic changes that occurred during the domestication and improvement of upland cotton remain poorly understood, and the available genetic resources from improved cotton cultivars are very limited. By applying restriction site-associated DNA marker sequencing (RAD-seq) technology to 582 tetraploid cotton accessions, we detected two distinct genomic signatures had the highest divergence on chromosomes A06 and A08 which dramaticly affect the population structure and genetic diversity in modern improved upland cotton populations. Based on integrating the pedigree of the accessions with previously reported QTLs, genome-wide association study (GWAS) and introgression analyses, we suggest that the two divergent regions resulted from the introgression of exotic lineages from G. hirsutum races and wild relatives. Genetic divergence of these regions were the typical genomic characteristic might be responsible for maturity in central Asia ecotype cotton population (Group-2) A06 and fiber quality for offspring resulting from interspecific hybridization developing mainly in southern China (Group-1) (A08), and several candidate genes were screened by integrating transcriptome data. Additionally, both genomic regions are located in putative pericentromere regions, implying that their application will be challenging. In the study, based on high-density SNP markers, we firstly reported two genomic signatures on chromosome A06 and A08 which could both distinguish ecotypes and be responsible for important agronomic traits in upland cotton. These results provides new insights for understanding the genomic basis of exotic introgressions in modern cotton cultivars.

Prospects for using primitive landrace germplasm for cotton improvement

Germplasm and Genetic Stocks
Authors: 
Campbell, Todd
Hugie, Kari
Paterson, Andrew
Shehzad,Tariq
Subramani, Jay
Abstract: 
Long-term cotton genetic improvement is dependent upon the careful introduction and exploitation of new genetic variation. One of the largely untapped reservoirs of genetic diversity available to cotton breeders resides in the primitive Gossypium hirsutum L. landrace collection. Although most accessions are classified as G. hirsutum and reside within the primary upland cotton gene pool, widespread use of these genetic resources has been minimal due to their photoperiodic nature and perennial growth habit. In our research program, we are deploying two different, but related approaches to introduce and use novel genetic variation present within this genetic resource. First, we are developing breeding populations derived from crosses involving a number of day-neutral converted lines developed by the USDA-ARS Mississippi State, MS research program. Second, we are characterizing a set of naturally occurring day-neutral primitive landrace accessions in an effort to identify novel accessions for use as breeding parents. Preliminary results suggest these genetic resources contain beneficial alleles for fiber quality and climate resiliency.

Utility of Germplasm from the NPGS in the Texas A&M University Cotton Breeding Program

Germplasm and Genetic Stocks
Authors: 
Hague, Steve
Abstract: 
The U.S. National Plant Germplasm System holds a wealth of valuable cotton germplasm available for breeders. The cotton breeding program at Texas A&M University has actively used numerous lines in its program as parent material over the last 12 years. Both Gossypium hirsutum and G. barbadense lines have been integrated into elite TAMU breeding material. By tracking the fate and value of the lines in terms of performance and creation of genetic variability, results indicate this source of germplasm has substantially benefited the program in terms of improving yield potential, fiber quality and host plant resistance.

Cotton beta-glucosidase gene GhBG1A coordinates fiber transition from elongation to secondary cell wall deposition

Structural Genomics
Authors: 
Shang, Xiaoguang
Wang, Haitang
Zhu, Lijie
Chai, Qichao
Yu, Yujia
Li, Shengmei
Guo, Wangzhen
Abstract: 
Abstract：Cotton fiber is the most important natural textile raw material in the world. It also represents an outstanding single-celled model for understanding plant cell elongation and cell wall and cellulose biosynthesis. Compared to extensive studies on fiber initiation and elongation processes, much less is known about the molecular basis underlying secondary cell wall cellulose deposition, a process profoundly impacting mature fiber properties. In this study, we identified a gene, GhBG1A, encoding glycosyl hydrolase family 3 beta-glucosidase, which coordinates cotton fiber elongation and cellulose deposition through regulating sugar metabolism. GhBG1A was preferentially expressed in cotton fibers and significantly associated with fiber length and strength. Overexpression of GhBG1A at fiber elongation stage significantly reduced fiber length, but remarkably increased cellulose biosynthesis leading to thicker fiber cell wall. Molecular and biochemical studies indicate that sucrose content and expression levels of cellulose biosynthesis related genes was evidently increased in transgenic cotton fibers. Moreover, using two cultivated tetraploid cotton species with distinctly different fiber qualities, higher transcript levels and enzyme activities of GhBG1A homologs were detected at fiber secondary cell wall (SCW) deposition stage in G. barbadense cv. H7124, which possesses elite fibers, than that in G. hirsutum acc. TM-1. Taken together, GhBG1A plays an important role in fiber transition from elongation to SCW deposition, and fine-tune overexpression of GhBG1A homolog at fiber SCW stage could improve fiber qualities in cotton fiber quality breeding program.

Detection of SNPs from Gossypium barbadense L. Cotton through whole-genome resequencing and their utilization

Structural Genomics
Authors: 
Ishwarappa, S Katageri
N V, Mohan Kumar
S, Anjan Gowda
Abstract: 
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

Development of high-density 80 K SNP array and its evaluation and application in G. hirsutum

Structural Genomics
Authors: 
Guo, Wangzhen
Cai, Caiping
Zhu, Guozhong
Zhang, Tianzhen
Abstract: 
High-throughput genotyping platforms play important roles in plant genomic studies. Cotton (Gossypium pp.) is the world’s important natural textile fiber and oil crop. Upland cotton accounts for more than 90% of the world’s cotton production, however, modern upland cotton cultivars have narrow genetic diversity. The amounts of genomic sequencing and re-sequencing data released make it possible to develop a high-quality single nucleotide polymorphism (SNP) array for intraspecific genotyping detection in cotton. Here we report a high-throughput CottonSNP80K array and its utilization in genotyping detection and targeted genes mining. 82,259 SNP markers were selected from the re-sequencing data of 100 cotton cultivars and used to produce the array on the Illumina Infinium platform. 77,774 SNP loci (94.55%) were successfully synthesized on the array. Of them, 77,252 (99.33%) had call rates of >95% in 352 cotton accessions and 59,502 (76.51%) were polymorphic loci. Application tests using 22 cotton accessions with parent/F1 combinations or with similar genetic backgrounds showed that CottonSNP80K array had high genotyping accuracy, good repeatability, and wide applicability. Phylogenetic analysis of 312 cotton cultivars and landraces with wide geographical distribution showed that they could be classified into ten groups, irrelevant of their origins. We found that the different landraces were clustered in different subgroups, indicating that these landraces were major contributors to the development of different breeding populations of modern G. hirsutum cultivars in China. We integrated a total of 54,588 SNPs (MAFs >0.05) associated with 10 salt stress traits into 288 G. hirsutum accessions for genome-wide association studies (GWAS), and eight significant SNPs associated with three salt stress traits were detected. Further, two genes located in the SNP regions were detected to distinctly related to salt tolerance, with significantly upregulated expression after salt treatment and significantly enhanced cotton susceptibility to salt stress after their silencing. Taken together, CottonSNP80K play important roles in germplasm genotyping, variety verification, functional genomics studies, and molecular breeding in cotton.

Diallel Analysis of Ekangmian 9 and Other Cotton Varieties Apparently Resistant to Fusarium Wilt and Tolerant to Verticillium Wilt

Structural Genomics
Authors: 
Liu,Yangai
Li,Wei
Hu,Aibin
Yang,Daigang*
Abstract: 
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

Dissection of a Verticillium wilt resistance QTL on chromosome At_chr9 in cotton (Gossypium hirsutum L.)

Structural Genomics
Authors: 
Wang Hongmei*, Zhao Yunlei, Chen Wei, Zhao Pei, Gong Haiyan, Cui Yanli, Sang Xiaohui, Lu Ningning, Zhang Kai
Abstract: 
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.

EMS-induced short cotton fiber mutant Ligon lintless-y (liy) and its genomic location

Structural Genomics
Authors: 
Fang, David
Naoumkina, Marina
Thyssen, Gregory
Bechere, Efrem
Li, Ping
Abstract: 
A short fiber mutant Ligon-lintless-y was created through seed treatment with ethyl methanesulfonate (EMS). Genetic analysis indicated that the mutation is controlled by a single recessive locus designated liy. Besides causing short seed fibers, the mutation also affects other traits including plant height. From an F2 mapping population, we selected 100 short fiber progeny (liy/liy), and bulked their DNAs. We sequenced this DNA bulk along with the two parents of the mapping population. The liy locus was mapped on chromosome A07. Flanking SNP/InDel markers were developed. We also evaluated global transcriptional changes during cotton fiber development at 3, 8 and 16 days post anthesis triggered by liy mutation. Gene set enrichment analysis revealed that many metabolic pathways, including carbohydrate, cell wall, hormone metabolism and transport were substantially altered in liy developing fibers. We discuss perturbed expression of genes involved in signal transduction and biosynthesis of phytohormones, such as auxin, abscisic acid, gibberellin and ethylene.