Genetic detection of node of first fruiting branch in crosses of a cultivar with two exotic accessions of upland cotton

Guo, Yufang; McCarty, Jack C.; Jenkins, Johnie N.; An, Chuanfu; Saha, Sukumar

doi:10.1007/s10681-008-9809-z

Cited by 25 publications

(22 citation statements)

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“…BNL 3008 was found to be associated with root‐knot nematode [ Meloidogyne incognita (Kofoid & White) Chitwood] resistance (Ulloa et al, 2016); BNL3379 (Bolek et al, 2005), CIR97 (Wang et al, 2014a), CIR218 (Zhang et al, 2015), and BNL3031 (Li et al, 2013) with verticilium wilt ( Verticillium dahliae Kleb. ) resistance; BNL 1404 (Mei et al, 2013) and BNL 256 (Kantartzi and Stewart, 2008) with lint percentage; BNL1693 with leaf shape gene (Lacape et al, 2013); and BNL852 with node of first fruiting branch (Guo et al, 2009). It is possible that some of these traits are distinguishing factors between the subpopulations.…”

Section: Resultsmentioning

confidence: 99%

Genetic Diversity and Population Structure in the Landrace Accessions of Gossypium hirsutum

2017

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In this study, genetic diversity and population structure was assessed in a set of 185 Gossypium hirsutum L. landrace accessions, collected mainly from Central America during the mid‐1900s using genomewide simple sequence repeat (SSR) markers. Genotyping the diversity panel using 122 SSRs detected 143 marker loci. A total of 819 alleles were identified across 143 markers loci, and out of these, 23.3% were unique alleles, observed only in one accession. Average genetic distance between accessions was 0.36, suggesting higher levels of genetic variation present in the cotton tropical landrace germplasm. Using Bayesian model‐based structure analysis, five major subgroups were identified that roughly corresponded to the geographical origins of accessions. Substantial admixture was observed as accessions from different geographical locations were grouped together. Results from phylogenetic analysis, principal component analysis, and analysis of molecular variance supported clustering based on STRUCTURE analysis. Pairwise kinship estimates suggested that most of the accessions were unrelated. Finally, core sets representing various levels of allelic richness were identified using POWERMARKER. Assessing genetic diversity, population structure, and identifying the core sets in the landraces will facilitate the utilization of unexploited tropical genetic diversity towards developing improved cotton cultivars.

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Section: Resultsmentioning

confidence: 99%

Genetic Diversity and Population Structure in the Landrace Accessions of Gossypium hirsutum

2017

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“…4b, Additional file 1: Figure S1b) were reported to be associated with fiber fineness (FTX) by Yu et al [48, 49]. In another independent QTL mapping effort, Guo et al [54] reported that BNL3071 marker, also tightly linked with PHYB dCAPS marker, was associated with the node of first fruiting branch (NFB) in a mapping population (F 2:5 ) from the cross between T1107 and T1354, a day-neutral cultivar Deltapine 61 and photoperiodic G. hirsutum accessions, respectively. These findings further suggest the importance of phytochrome and light signal transduction for both fiber development and for flowering time/earliness in cotton.…”

Section: Resultsmentioning

confidence: 99%

Development, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers

Kushanov

Pepper

et al. 2016

BMC Genet

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BackgroundAmong SNP markers that become increasingly valuable in molecular breeding of crop plants are the CAPS and dCAPS markers derived from the genes of interest. To date, the number of such gene-based markers is small in polyploid crop plants such as allotetraploid cotton that has A- and D-sub-genomes. The objective of this study was to develop and map new CAPS and dCAPS markers for cotton developmental-regulatory genes that are important in plant breeding programs.Results Gossypium hirsutum and G. barbadense, are the two cultivated allotetraploid cotton species. These have distinct fiber quality and other agronomic traits. Using comparative sequence analysis of characterized GSTs of the PHYA1, PHYB, and HY5 genes of G. hirsutum and G. barbadense one PHYA1-specific Mbo I/Dpn II CAPS, one PHYB-specific Alu I dCAPS, and one HY5-specific Hinf I dCAPS cotton markers were developed. These markers have successfully differentiated the two allotetraploid genomes (AD1 and AD2) when tested in parental genotypes of ‘Texas Marker-1’ (‘TM-1’), ‘Pima 3–79’ and their F1 hybrids. The genetic mapping and chromosome substitution line-based deletion analyses revealed that PHYA1 gene is located in A-sub-genome chromosome 11, PHYB gene is in A-sub-genome chromosome 10, and HY5 gene is in D-sub-genome chromosome 24, on the reference ‘TM-1’ x ‘Pima 3–79’ RIL genetic map. Further, it was found that genetic linkage map regions containing phytochrome and HY5-specific markers were associated with major fiber quality and flowering time traits in previously published QTL mapping studies.ConclusionThis study detailed the genome mapping of three cotton phytochrome genes with newly developed CAPS and dCAPS markers. The proximity of these loci to fiber quality and other cotton QTL was demonstrated in two A-subgenome and one D-subgenome chromosomes. These candidate gene markers will be valuable for marker-assisted selection (MAS) programs to rapidly introgress G. barbadense phytochromes and/or HY5 gene (s) into G. hirsutum cotton genotypes or vice versa.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0448-4) contains supplementary material, which is available to authorized users.

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“…In particular, QTLs for FBP, WGP, NFFB, HNFFB and PH were detected as follows: QTLs for FBP on chromosomes A3, A7, A8/D8, A9, A13, D3, D4 and D7 [38]; QTLs for WGP on chromosomes A13, D3 and D8 [38]; QTLs for NFFB on chromosomes A1, A5, A6, A9, A10, A11, A13, D1, D3, D6, D7, D9 and D11 [37, 39, 41]; QTLs for HNFFB on chromosomes A9, D3 and D6 [37]; and QTLs for PH on chromosomes A3, A4, A5, A9, A11, A13, D2, D3, D4, D5, D6, D8, D9 and D11 [36, 42]. These results indicate that D3 contains QTLs for FBP, WGP, NFFB, HNFFB and PH, which suggests that D3 is one of the chromosomes responsible for cotton earliness.…”

Section: Discussionmentioning

confidence: 99%

High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L

et al. 2016

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Background Gossypium hirsutum L., or upland cotton, is an important renewable resource for textile fiber. To enhance understanding of the genetic basis of cotton earliness, we constructed an intra-specific recombinant inbred line population (RIL) containing 137 lines, and performed linkage map construction and quantitative trait locus (QTL) mapping.ResultsUsing restriction-site associated DNA sequencing, a genetic map composed of 6,434 loci, including 6,295 single nucleotide polymorphisms and 139 simple sequence repeat loci, was developed from RIL population. This map spanned 4,071.98 cM, with an average distance of 0.63 cM between adjacent markers. A total of 247 QTLs for six earliness-related traits were detected in 6 consecutive years. In addition, 55 QTL coincidence regions representing more than 60 % of total QTLs were found on 22 chromosomes, which indicated that several earliness-related traits might be simultaneously improved. Fine-mapping of a 2-Mb region on chromosome D3 associated with five stable QTLs between Marker25958 and Marker25963 revealed that lines containing alleles derived from CCRI36 in this region exhibited smaller phenotypes and earlier maturity. One candidate gene (EMF2) was predicted and validated by quantitative real-time PCR in early-, medium- and late-maturing cultivars from 3- to 6-leaf stages, with highest expression level in early-maturing cultivar, CCRI74, lowest expression level in late-maturing cultivar, Bomian1.ConclusionsWe developed an SNP-based genetic map, and this map is the first high-density genetic map for short-season cotton and has the potential to provide deeper insights into earliness. Cotton earliness-related QTLs and QTL coincidence regions will provide useful materials for QTL fine mapping, gene positional cloning and MAS. And the gene, EMF2, is promising for further study.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3269-y) contains supplementary material, which is available to authorized users.

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Genetic detection of node of first fruiting branch in crosses of a cultivar with two exotic accessions of upland cotton

Cited by 25 publications

References 57 publications

Genetic Diversity and Population Structure in the Landrace Accessions of Gossypium hirsutum

Genetic Diversity and Population Structure in the Landrace Accessions of Gossypium hirsutum

Development, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers

High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L

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