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1. A GWAS identified a major QTL for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in a MAGIC population of Upland cotton and a meta-analysis of QTLs for Fusarium wilt resistance

Author:
David D. Fang,   et al.   ; Yi Zhu; Gregory N. Thyssen; Abdelraheem Abdelraheem; Zonghua Teng; Johnie N. Jenkins; Jack C. McCarty; Tom Wedegaertner; Kater Hake; Jinfa Zhang;     Show all 10 Authors
Source:
Theoretical and applied genetics 2022 v.135 no.7 pp. 2297-2312
ISSN:
0040-5752
Subject:
Fusarium oxysporum f. sp. vasinfectum; Fusarium wilt; Gossypium hirsutum; chromosomes; cotton; cultivars; genes; genome-wide association study; genomics; meta-analysis; phenotype
Abstract:
... KEY MESSAGE: A major QTL conferring resistance to Fusarium wilt race 4 in a narrow region of chromosome D02 was identified in a MAGIC population of 550 RILs of Upland cotton. Numerous studies have been conducted to investigate the genetic basis of Fusarium wilt (FW, caused by Fusarium oxysporum f. sp. vasinfectum, FOV) resistance using bi-parental and association mapping populations in cotton. In ...
DOI:
10.1007/s00122-022-04113-z

2. Mapping-by-sequencing the locus of EMS-induced mutation responsible for tufted-fuzzless seed phenotype in cotton

Author:
David D. Fang,   et al.   ; Marina Naoumkina; Gregory N. Thyssen; Efrem Bechere; Ping Li; Christopher B. Florane;     Show all 6 Authors
Source:
Molecular genetics and genomics 2021 v.296 no.5 pp. 1041-1049
ISSN:
1617-4615
Subject:
DNA; cell growth; ethyl methanesulfonate; fiber cells; gene expression regulation; genetic analysis; genomics; growth and development; lint cotton; loci; mutagenesis; mutants; nucleotide sequences; phenotype; progeny
Abstract:
... Cotton fiber mutants are valuable resources for studying functions of altered genes and their roles in fiber development. The n₄ᵗ is a recessive tufted-fuzzless seed mutant created through chemical mutagenesis with ethyl methanesulfonate. Genetic analysis indicated that the tufted-fuzzless phenotype is controlled by a single recessive locus. In this study, we developed an F₂ population of 602 prog ...
DOI:
10.1007/s00438-021-01802-0

3. Stability and transferability assessment of the cotton fiber strength QTL qFS-c7-1 on chromosome A07

Author:
David D. Fang,   et al.   ; Linghe Zeng; Gregory N. Thyssen; Christopher D. Delhom; Efrem Bechere; Don C. Jones; Ping Li;     Show all 7 Authors
Source:
crop journal 2021 v.9 no.2 pp. 380-386
ISSN:
2214-5141
Subject:
breeding programs; chromosomes; crossing; cultivars; fiber content; genetic markers; inbred lines; length; lint cotton; marker-assisted selection; micronaire; parents; phenotypic variation; population; progeny; seeds
Abstract:
... Previously we identified a major cotton fiber strength QTL (qFS-c7-1) on chromosome A07 using a multi-parent advanced generation intercross (MAGIC) population. To assess the stability and transferability of this QTL and its utility in cotton breeding, we made ten new populations. These populations were developed from crosses between MAGIC recombinant inbred lines, or between cotton cultivars that ...
DOI:
10.1016/j.cj.2020.06.016

4. GWAS reveals consistent QTL for drought and salt tolerance in a MAGIC population of 550 lines derived from intermating of 11 Upland cotton (Gossypium hirsutum) parents

Author:
David D. Fang,   et al.   ; Abdelraheem Abdelraheem; Gregory N. Thyssen; Johnie N. Jenkins; Jack C. McCarty; Tom Wedegaertner; Jinfa Zhang;     Show all 7 Authors
Source:
Molecular genetics and genomics 2021 v.296 no.1 pp. 119-129
ISSN:
1617-4615
Subject:
Gossypium hirsutum; chromosomes; cotton; cultivars; drought; drought tolerance; genomics; greenhouses; marker-assisted selection; plant height; quantitative traits; salt stress; salt tolerance; seedlings; stress tolerance; transgressive segregation; water stress
Abstract:
... Cotton is grown in arid and semi-arid regions where abiotic stresses such as drought and salt are prevalent. There is a lack of studies that simultaneously address the genetic and genomic basis of tolerance to drought and salt stress. In this study, a multi-parent advanced generation inter-cross (MAGIC) population of 550 recombinant inbred lines (RILs) together with their 11 Upland cotton parents ...
DOI:
10.1007/s00438-020-01733-2

5. QTL analysis of agronomic, fiber quality, and abiotic stress tolerance traits in a recombinant inbred population of pima cotton

Author:
David D. Fang,   et al.   ; Abdelraheem Abdelraheem; Jane Dever; Jinfa Zhang;     Show all 4 Authors
Source:
Crop science 2020 v.60 no.4 pp. 1823-1843
ISSN:
0011-183X
Subject:
Gossypium barbadense; abiotic stress; chromosome mapping; cotton; drought; fiber quality; genomics; greenhouses; marker-assisted selection; microsatellite repeats; quantitative traits; salt tolerance; stress tolerance
Abstract:
... Pima cotton (Gossypium barbadense L.) is grown for its superior fiber quality in four U.S. states and in several other countries. However, there is a lack of information on major and stable quantitative trait loci (QTL) for fiber quality and agronomic traits and abiotic stress tolerance across different environments. In this study, a genetic linkage map based on 403 simple sequence repeat (SSR) ma ...
DOI:
10.1002/csc2.20153

6. Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation

Author:
David D. Fang,   et al.   ; Liuling Pei; Xianhui Huang; Zhenping Liu; Xuehan Tian; Jiaqi You; Jianying Li; Keith Lindsey; Longfu Zhu; Xianlong Zhang; Maojun Wang;     Show all 11 Authors
Source:
Genome biology 2022 v.23 no.1 pp. 45
ISSN:
1474-760X
Subject:
allotetraploidy; cell differentiation; chromatin; genes; lint cotton; topology; transcription (genetics)
Abstract:
... BACKGROUND: Despite remarkable advances in our knowledge of epigenetically mediated transcriptional programming of cell differentiation in plants, little is known about chromatin topology and its functional implications in this process. RESULTS: To interrogate its significance, we establish the dynamic three-dimensional (3D) genome architecture of the allotetraploid cotton fiber, representing a ty ...
Handle:
10113/7665675
DOI:
10.1186/s13059-022-02616-y

7. Elucidation of sequence polymorphism in fuzzless-seed cotton lines

Author:
David D. Fang,   et al.   ; Marina Naoumkina; Gregory N. Thyssen; Ping Li; Christopher B. Florane;     Show all 5 Authors
Source:
Molecular genetics and genomics 2021 v.296 no.1 pp. 193-206
ISSN:
1617-4615
Subject:
DNA; cultivars; genes; genomics; lint cotton; loci; mutants; seed coat; textile industry
Abstract:
... Most commercially produced cotton cultivars have two types of fibers on the seed coat, short fuzz and long lint. Lint fiber is used in the textile industry, while fuzz is considered an undesirable trait. Both types of fibers are believed to be controlled by the same regulators; however, their mechanisms of actions are still obscure. Cotton fiber mutants provide an excellent system to study the gen ...
DOI:
10.1007/s00438-020-01736-z

8. An EMS-induced mutation in a tetratricopeptide repeat-like superfamily protein gene (Ghir_A12G008870) on chromosome A12 is responsible for the liy short fiber phenotype in cotton

Author:
David D. Fang,   et al.   ; Marina Naoumkina; Gregory N. Thyssen; Efrem Bechere; Ping Li; Christopher B. Florane;     Show all 6 Authors
Source:
Theoretical and applied genetics 2020 v.133 no.1 pp. 271-282
ISSN:
0040-5752
Subject:
DNA; Gossypium hirsutum; alleles; amino acid substitution; breeding lines; chromosome mapping; crossbreds; crossing; ethyl methanesulfonate; gene silencing; genetic analysis; genetic markers; induced mutation; isoleucine; linkage (genetics); lint cotton; loci; mutants; nucleotide sequences; phenotype; progeny; recessive genes; reverse transcriptase polymerase chain reaction; seeds; single nucleotide polymorphism; tetratricopeptide repeats; threonine
Abstract:
... KEY MESSAGE: The EMS-induced threonine/isoleucine substitution in a tetratricopeptide repeat-like superfamily protein encoded by gene Ghir_A12G008870 is responsible for the Ligon-lintless-y (liy) short fiber phenotype in cotton. A short fiber mutant Ligon-lintless-y was created through treating the seeds of the cotton line MD15 with ethyl methanesulfonate. Genetic analysis indicated that the short ...
Handle:
10113/6808414
DOI:
10.1007/s00122-019-03456-4

9. Effects of inter‐species chromosome substitution on cottonseed mineral and protein nutrition profiles

Author:
David D. Fang,   et al.   ; Zhongqi He; Hailin Zhang; Linghe Zeng; Johnie N. Jenkins; Jack C. McCarty;     Show all 6 Authors
Source:
Agronomy journal 2020 v.112 no.5 pp. 3963-3974
ISSN:
0002-1962
Subject:
Gossypium barbadense; Gossypium hirsutum; boron; calcium; chromosome substitution; copper; cottonseed; cultivars; inbred lines; interspecific hybridization; introgression; iron; magnesium; manganese; mineral content; nickel; phosphorus; plant micronutrients; plant proteins; potassium; protein content; sodium; substitution lines; sulfur; zinc
Abstract:
... Upland cotton (Gossypium hirsutum L.) is the major species of cotton due to its high yield and good adaptability. With much less land area, pima cotton (G. barbadense L.) is also cultivated for its superior fibers. Existing research efforts have mainly focused on introgression of fiber quality traits from pima into upland cotton, with few on the seed mineral and protein contents. In this research, ...
Handle:
10113/7222891
DOI:
10.1002/agj2.20264

10. Application of the Cottonscope for determining fiber maturity and fineness of an upland cotton MAGIC population

Author:
David D. Fang,   et al.   ; Hee Jin Kim; Christopher D. Delhom; Linghe Zeng; Johnie N. Jenkins; Jack C. McCarty; Don C. Jones;     Show all 7 Authors
Source:
Crop science 2020 v.60 no.5 pp. 2266-2279
ISSN:
0011-183X
Subject:
Gossypium hirsutum; advanced fiber information system; cotton; fabrics; fiber quality; fineness; genomics; lint yield; phenotype; technology
Abstract:
... Fineness and maturity are two cotton (Gossypium spp.) fiber properties that respectively estimate the fiber diameter and degree of internal fiber thickening. Cotton researchers have been searching for accurate and efficient ways of measuring them due to their important roles in lint yield, fiber quality, and downstream textile performance. The recent development of the Cottonscope has offered an i ...
DOI:
10.1002/csc2.20197

11. Quantitative trait locus mapping of drought and salt tolerance in an introgressed recombinant inbred line population of Upland cotton under the greenhouse and field conditions

Author:
David D. Fang,   et al.   ; Abdelraheem Abdelraheem; Jinfa Zhang;     Show all 3 Authors
Source:
Euphytica 2018 v.214 no.1 pp. 8
ISSN:
0014-2336
Subject:
Gossypium barbadense; Gossypium hirsutum; biotic stress; chromosome mapping; cotton; drought; drought tolerance; environmental factors; fiber quality; genes; genetic markers; greenhouse experimentation; greenhouses; hybrids; inbred lines; introgression; lint yield; loci; marker-assisted selection; microsatellite repeats; parents; phenotypic variation; plant breeding; plant growth; quantitative trait loci; salt stress; salt tolerance; seedlings; stress tolerance
Abstract:
... Drought and salt tolerances are complex traits and controlled by multiple genes, environmental factors and their interactions. Drought and salt stresses can result in more than 50% yield loss in Upland cotton (Gossypium hirsutum L.). G. barbadense L. (the source of Pima cotton) carries desirable traits such as tolerance to abiotic and biotic stress along with high fiber quality. However, few studi ...
DOI:
10.1007/s10681-017-2095-x

12. Unraveling Cotton Fiber Development Using Fiber Mutants in the Post‐Genomic Era

Author:
David D. Fang,   et al.   ; Marina Naoumkina; Hee Jin Kim;     Show all 3 Authors
Source:
Crop science 2018 v.58 no.6 pp. 2214-2228
ISSN:
0011-183X
Subject:
Gossypium; actin; biosynthesis; cell walls; cellulose; chromosome mapping; cytoskeleton; energy; genes; growth and development; lint cotton; models; mutants; mutation; ovules; phenotype; plant hormones; synthetic fibers; transcription factors; transcriptomics; trichomes
Abstract:
... Cotton (Gossypium spp.) fibers are unicellular trichomes that differentiate from ovule epidermal cells. Cotton fiber development is divided into four distinct yet overlapping stages: initiation, elongation, secondary cell wall (SCW) biosynthesis, and maturation. There are numerous naturally occurring and man‐made fiber mutants that display aberrant phenotypes ranging from fiberless to extremely sh ...
DOI:
10.2135/cropsci2018.03.0184

13. Evaluation of genomic selection methods for predicting fiber quality traits in Upland cotton

Author:
David D. Fang,   et al.   ; Md Sariful Islam; Johnie N. Jenkins; Jia Guo; Jack C. McCarty; Don C. Jones;     Show all 6 Authors
Source:
Molecular genetics and genomics 2020 v.295 no.1 pp. 67-79
ISSN:
1617-4615
Subject:
Bayesian theory; Gossypium hirsutum; fiber quality; genomics; genotyping; heritability; lint cotton; marker-assisted selection; phenotype; population size; prediction; progeny
Abstract:
... The use of genomic selection (GS) has stimulated a new way to utilize molecular markers in breeding for complex traits in the absence of phenotypic data. GS can potentially decrease breeding cycle by selecting the progeny in the early stages. The objective of this study was to experimentally evaluate the potential value of genomic selection in Upland cotton breeding. Six fiber quality traits were ...
DOI:
10.1007/s00438-019-01599-z

14. Mapping and validation of a fiber length QTL on chromosome D11 using two independent F2 populations of upland cotton

Author:
David D. Fang,   et al.   ; Marina Naoumkina; Linghe Zeng; Maojun Wang; Gregory N. Thyssen; Christopher B. Florane; Ping Li; Christopher D. Delhom;     Show all 8 Authors
Source:
Molecular breeding 2020 v.40 no.3 pp. 31
ISSN:
1380-3743
Subject:
Gossypium hirsutum; chromosomes; cotton; genome-wide association study; marker-assisted selection; phenotype; quantitative traits
Abstract:
... The analysis of association between genotypic markers and phenotypic traits allows identification of quantitative trait loci (QTLs), which can be applied through marker-assisted selection in breeding programs to improve the quality of crops. However, success in these applications depends primarily on the stability and dominance of the QTL. We previously identified a significant fiber length (FL) Q ...
DOI:
10.1007/s11032-020-01111-1

15. Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton

Author:
David D. Fang,   et al.   ; Zhonghua Li; Pengcheng Wang; Chunyuan You; Jiwen Yu; Xiangnan Zhang; Feilin Yan; Zhengxiu Ye; Chao Shen; Baoqi Li; Kai Guo; Nian Liu; Gregory N. Thyssen; Keith Lindsey; Xianlong Zhang; Maojun Wang; Lili Tu;     Show all 17 Authors
Source:
new phytologist 2020 v.226 no.6 pp. 1738-1752
ISSN:
0028-646X
Subject:
allotetraploidy; cell growth; cell walls; fiber quality; gene regulatory networks; genome-wide association study; lint cotton; loci; quantitative trait loci; transcription (genetics); transcriptome
Abstract:
... The cotton fibre serves as a valuable experimental system to study cell wall synthesis in plants, but our understanding of the genetic regulation of this process during fibre development remains limited. We performed a genome‐wide association study (GWAS) and identified 28 genetic loci associated with fibre quality in allotetraploid cotton. To investigate the regulatory roles of these loci, we seq ...
DOI:
10.1111/nph.16468

16. A novel variant of Gh_D02G0276 is required for root-knot nematode resistance on chromosome 14 (D02) in Upland cotton

Author:
David D. Fang,   et al.   ; Martin J. Wubben; Gregory N. Thyssen; Franklin E. Callahan; Dewayne D. Deng; Jack C. McCarty; Ping Li; Md Sariful Islam; Johnie N. Jenkins;     Show all 9 Authors
Source:
Theoretical and applied genetics 2019 v.132 no.5 pp. 1425-1434
ISSN:
0040-5752
Subject:
Gossypium hirsutum; Meloidogyne incognita; alleles; bacterial proteins; biotic stress; breeding programs; cotton; egg production; enzymes; gene silencing; genetic markers; germplasm; inbred lines; loci; marker-assisted selection; mutation; peptides; phenotype; resistance genes; resistance mechanisms; root-knot nematodes; Southeastern United States
Abstract:
... KEY MESSAGE: MAGIC population sequencing and virus-induced gene silencing identify Gh_D02G0276 as a novel root-knot nematode resistance gene on chromosome 14 in Upland cotton. The southern root-knot nematode [RKN; Meloidogyne incognita (Kofoid & White)] remains the primary yield-limiting biotic stress to Upland cotton (Gossypium hirsutum L.) throughout the southeastern USA. While useful genetic ma ...
DOI:
10.1007/s00122-019-03289-1

17. Role of xyloglucan in cotton (Gossypium hirsutum L.) fiber elongation of the short fiber mutant Ligon lintless-2 (Li2)

Author:
David D. Fang,   et al.   ; Marina Naoumkina; Doug J. Hinchliffe; Christopher B. Florane; Gregory N. Thyssen;     Show all 5 Authors
Source:
Gene 2017 v.626 pp. 227-233
ISSN:
0378-1119
Subject:
Gossypium hirsutum; biosynthesis; cellulose microfibrils; embryophytes; enzymes; fiber cells; flowering; gene expression regulation; genes; lint cotton; models; mutants; mutation; pleiotropy; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; vegetative growth; xyloglucans
Abstract:
... Xyloglucan is a matrix polysaccharide found in the cell walls of all land plants. In growing cells, xyloglucan is thought to connect cellulose microfibrils and regulate their separation during wall extension. Ligon lintless-2 (Li2) is a monogenic dominant cotton fiber mutation that causes extreme reduction in lint fiber length with no pleiotropic effects on vegetative growth. Li2 represents an exc ...
DOI:
10.1016/j.gene.2017.05.042
CHORUS:
10.1016/j.gene.2017.05.042
Chorus Open Access:
10.1016/j.gene.2017.05.042

18. Genome-wide analysis of gene expression of EMS-induced short fiber mutant Ligon lintless-y (liy) in cotton (Gossypium hirsutum L.)

Author:
David D. Fang,   et al.   ; Marina Naoumkina; Efrem Bechere; Gregory N. Thyssen; Christopher B. Florane;     Show all 5 Authors
Source:
Genomics 2017 v.109 no.3-4 pp. 320-329
ISSN:
0888-7543
Subject:
Gossypium hirsutum; abscisic acid; auxins; biochemical pathways; biosynthesis; cell walls; ethylene; flowering; gene expression; gene expression regulation; genes; gibberellins; hormone metabolism; lint cotton; loci; mutants; signal transduction; transcription (genetics)
Abstract:
... In this work we describe a chemically-induced short fiber mutant cotton line, Ligon-lintless-y (liy), which is controlled by a single recessive locus and affects multiple traits, including height of the plant, and length and maturity of fiber. An RNAseq analysis was used to evaluate global transcriptional changes during cotton fiber development at 3, 8 and 16days post anthesis. We found that 613, ...
DOI:
10.1016/j.ygeno.2017.05.007
CHORUS:
10.1016/j.ygeno.2017.05.007

19. Quantitative trait loci analysis for net ginning energy requirements in upland cotton (Gossypium hirsutum L.)

Author:
David D. Fang,   et al.   ; Efrem Bechere; Hirut Kebede; Robert G. Hardin IV; Md. S. Islam; Ping Li; Jodi Scheffler;     Show all 7 Authors
Source:
Euphytica 2017 v.213 no.7 pp. 160
ISSN:
0014-2336
Subject:
Gossypium hirsutum; chromosome mapping; cotton; cultivars; electric power; energy; energy requirements; fiber quality; genetic markers; high volume instruments; leaves; loci; marker-assisted selection; microsatellite repeats; parents; phenotypic variation; plant breeding; progeny; quantitative trait loci; reciprocal crosses
Abstract:
... Cotton cultivars with reduced fiber-seed attachment force have the potential to be ginned faster with less energy. The objective of this study was to identify quantitative trait loci (QTL) for net ginning energy requirement (NGE), and its relationship with other fiber quality traits in upland cotton. Two cotton lines, TAM 182-34 ELS and AR 9317-26, with significant differences in NGE and fiber-see ...
DOI:
10.1007/s10681-017-1951-z

20. The P450 gene CYP749A16 is required for tolerance to the sulfonylurea herbicide trifloxysulfuron sodium in cotton (Gossypium hirsutum L.)

Author:
David D. Fang,   et al.   ; Gregory N. Thyssen; Marina Naoumkina; Jack C. McCarty; Johnie N. Jenkins; Christopher Florane; Ping Li;     Show all 7 Authors
Source:
BMC plant biology 2018 v.18 no.1 pp. 186
ISSN:
1471-2229
Subject:
Gossypium hirsutum; agricultural productivity; chromosomes; cotton; crop production; crops; cultivars; cytochrome P-450; evolution; exons; farmers; gene silencing; genetic markers; genotype; herbicide resistance; inbred lines; metabolism; phenotype; progeny; sodium; trifloxysulfuron; weed control
Abstract:
... BACKGROUND: Weed management is critical to global crop production and is complicated by rapidly evolving herbicide resistance in weeds. New sources of herbicide resistance are needed for crop plants so that applied herbicides can be rotated or combined to thwart the evolution of resistant weeds. The diverse family of cytochrome P450 proteins has been suggested to be a source of detoxifying herbici ...
DOI:
10.1186/s12870-018-1414-2
PubMed:
30200872
PubMed Central:
PMC6131939