Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)

Zhang, Zhen; Shāng, Hǎihóng; Shí, Yùzhēn; Huang, Long; Lǐ, Jùnwén; Gě, Qún; Gōng, Jǔwǔ; Liú, Àiyīng; Chen, Tingting; Wang, Dan; Wang, Yanling; Palanga, Koffi Kibalou; Jamshed, Muhammad; Li, Weijie; Lú, Quánwěi; Dèng, Xiǎoyīng; Tan, Yunna; Song, Weiwu; Cai, Juan; Li, Pengtao; Rashid, Harun Or; Gǒng, Wànkuí; Yuán, Yǒulù

doi:10.1186/s12870-016-0741-4

Cited by 122 publications

(108 citation statements)

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“…SD has previously been reported in interspecific populations of cotton (Guo et al, 2007; Blenda et al, 2012; Byers et al, 2012; Liang et al, 2012; Yu et al, 2013; Diouf et al, 2014; Zhang et al, 2014; Li et al, 2016), intraspecific populations of G. barbadense (Wang et al, 2013), intraspecific populations of G. hirsutum (Lin et al, 2009; Zhang et al, 2012, 2016; Ning et al, 2014), and intraspecific populations of G. arboreum (Li et al, 2007); however, the genetic mechanism of SD in cotton remains unclear.…”

Section: Discussionmentioning

confidence: 97%

Identification and Characterization of Segregation Distortion Loci on Cotton Chromosome 18

et al. 2017

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Segregation distortion is commonly detected via genetic mapping and this phenomenon has been reported in many species. However, the genetic causes of the segregation distortion regions in a majority of species are still unclear. To genetically dissect the SD on chromosome 18 in cotton, eight reciprocal backcross populations and two F2 populations were developed. Eleven segregation distortion loci (SDL) were detected in these ten populations. Comparative analyses among populations revealed that SDL18.1 and SDL18.9 were consistent with male gametic competition; whereas SDL18.4 and SDL18.11 reflected female gametic selection. Similarly, other SDL could reflect zygotic selection. The surprising finding was that SDL18.8 was detected in all populations, and the direction was skewed towards heterozygotes. Consequently, zygotic selection or heterosis could represent the underlying genetic mechanism for SDL18.8. Among developed introgression lines, SDL18.8 was introgressed as a heterozygote, further substantiating that a heterozygote state was preferred under competition. Six out of 11 SDL on chromosome 18 were dependent on the cytoplasmic environment. These results indicated that different SDL showed varying responses to the cytoplasmic environment. Overall, the results provided a novel strategy to analyze the molecular mechanisms, which could be further exploited in cotton interspecific breeding programs.

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Section: Discussionmentioning

confidence: 97%

Identification and Characterization of Segregation Distortion Loci on Cotton Chromosome 18

et al. 2017

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“…Hulse-Kemp et al constructed an ultra-high density genetic map using SNP arrays for marker detection and constructed a high-density genetic map consisting of 19,191 markers with 0.21 cM between adjacent markers [46]. Zhang et al constructed a high-density genetic map that contained 5,521 SNPs with an average marker density of 0.78 cM [47]. Thus, high-throughput sequencing techniques are more efficient.…”

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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“…In another report (Ning et al, 2013) the genetic map with 279 markers only covered about 35% of the cotton genome. The use of SNP markers and their applications to the marker assisted selection (MAS) allow to circumvent the problem of low genome coverage of intraspecific genetic map and to construct high density genetic map (Wei et al, 2014; Zhang et al, 2014b, 2016). So far, only one study (Fang et al, 2013b) has used a map covering more than 50% of the cotton genome (55.7%).…”

Section: Discussionmentioning

confidence: 99%

“…The cross was made in 2001 and a RIL population was developed by multiple cycles of selfing as described elsewhere (Sun et al, 2012; Jamshed et al, 2016; Zhang et al, 2016). Both parents showed some tolerance to VW some years while susceptible in other in natural field conditions on the experimental farm of the Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICRCAAS) located in Anyang, Henan province of China.…”

Section: Methodsmentioning

confidence: 99%

Quantitative Trait Locus Mapping for Verticillium wilt Resistance in an Upland Cotton Recombinant Inbred Line Using SNP-Based High Density Genetic Map

et al. 2017

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Verticillium wilt (VW) caused by Verticillium dahlia Kleb is one of the most destructive diseases of cotton. Numerous efforts have been made to improve the resistance of upland cotton against VW, with little progress achieved due to the paucity of upland cotton breeding germplasms with high level of resistance to VW. Gossypium barbadense was regarded as more resistant compared to upland cotton; however, it is difficult to apply the resistance from G. barbadense to upland cotton improvement because of the hybrid breakdown and the difficulty to fix resistant phenotype in their interspecific filial. Here we reported QTLs related to VW resistance identified in upland cotton based on 1 year experiment in greenhouse with six replications and 4 years investigations in field with two replications each year. In total, 119 QTLs of disease index (DI) and of disease incidence (DInc) were identified on 25 chromosome of cotton genome except chromosome 13 (c13). For DI, 62 QTLs explaining 3.7–12.2% of the observed phenotypic variations were detected on 24 chromosomes except c11 and c13. For DInc, 59 QTLs explaining 2.3–21.30% of the observed PV were identified on 19 chromosomes except c5, c8, c12-c13, c18-c19, and c26. Seven DI QTLs were detected to be stable in at least environments, among which six have sGK9708 alleles, while 28 DInc QTLs were detected to be stable in at least environments. Eighteen QTL clusters containing 40 QTLs were identified on 13 chromosomes (c1-c4, c6-c7, c10, c14, c17 c20-c22, and c24-c25). Most of the stable QTLs aggregated into these clusters. These QTLs and clusters identification can be an important step toward Verticillium wilt resistant gene cloning in upland cotton and provide useful information to understand the complex genetic bases of Verticillium wilt resistance.

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Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)

Cited by 122 publications

References 42 publications

Identification and Characterization of Segregation Distortion Loci on Cotton Chromosome 18

Identification and Characterization of Segregation Distortion Loci on Cotton Chromosome 18

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

Quantitative Trait Locus Mapping for Verticillium wilt Resistance in an Upland Cotton Recombinant Inbred Line Using SNP-Based High Density Genetic Map

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