Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq

Shen, Chao; Jin, Xin; Zhu, De; Lin, Zhongxu

doi:10.1186/s12864-017-3643-4

Cited by 31 publications

(31 citation statements)

References 55 publications

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“…This phenomenon may be because of A subgenome being approximately twice the size of D subgenome. In addition, homozygous SNPs and InDels accounted for a large proportion of these variations ( Figure S1A,B), which was consistent with a previous report in cotton [50].…”

Section: Discussionsupporting

confidence: 92%

“…Similar results were detected in maize [52], wheat [53], and cotton [54]. Furthermore, the ratio of non-synonymous to synonymous SNPs for 9053 and sGK9708 was 1.15 and 1.18, respectively, similar to the ratio found previously in rice (1.15) [41] and soybean (1.10) [55], and lower than previously reported for cotton (1.42-1.91) [50]. For InDels, in this study, the length of InDels ranged from 1 to 60 bp, which was longer than for rice [41] and sorghum [16] and was similar to soybean [55].…”

Section: Discussionsupporting

confidence: 89%

“…This may be associated with the greater tolerance of transitions to natural selection because of their conformational advantage relative to transversions that may better maintain protein structures [51]. In our study, the Ts/Tv ratio of 9053 and sGK9708 was 2.13 and 2.17, respectively, slightly lower than in rice (2.34) [41] and cotton (2.315) [50] identified previously. Additionally, the number of A/G transitions was slightly higher than C/T transitions while A/T transversions were the most common transversion.…”

Section: Discussioncontrasting

confidence: 50%

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Genome Resequencing Reveals Genetic Variation between the Parents of An Elite Hybrid Upland Cotton

Song

Wang

et al. 2018

Agronomy

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Cotton is one of the most important economic crops worldwide. As the global demands rising, cotton yield improvement is the most important goal of cotton breeding. Hybrids have great potential for increasing yield, however, the genetic mechanism of hybrids is still not clear. To investigate the genetic basis of cotton hybrids, we resequenced 9053 and sGK9708 with 62.13x coverage depth, the parents of the elite hybrid cotton CCRI63 that has obvious heterosis in lint percentage (LP) and boll weight (BW). Based on the cotton reference genome (TM-1), 1,287,661 single nucleotide polymorphisms (SNPs) and 152,479 insertions/deletions (InDels) were identified in 9053, and 1,482,784 SNPs and 152,985 InDels in sGK9708. Among them, 8649 SNPs and 629 InDels in the gene coding regions showed polymorphism between parents. Moreover, these variations involved 5092 genes, and 3835 of these genes were divided into 10 clusters based on the gene expression profiles. The genes in Cluster 3 and 7 were specifically expressed in the ovule and fiber development stage, suggesting that they might relate to LP and BW. We further co-localized the polymorphic SNPs and InDels with the reported quantitative trait loci (QTLs) of LP and BW, and identified 68 genes containing the polymorphic SNPs or InDels within these QTL intervals and as being related to fiber development. This suggested that the outstanding traits of CCRI63 such as LP and BW might be generated by accumulating the favorable variations from the parents. The results generated herein provide a genetic basis for cotton hybrids and genetic markers for marker-assisted selection breeding of cotton.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionsupporting

confidence: 89%

Section: Discussioncontrasting

confidence: 50%

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Genome Resequencing Reveals Genetic Variation between the Parents of An Elite Hybrid Upland Cotton

Song

Wang

et al. 2018

Agronomy

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“…TM‐1) (Zhang et al ., ) employing BWA software. SNP calling was conducted using the Genome Analysis Toolkit (version 3.1.1) and SAMtools/BCFtools software (Li, ; Li et al ., ), using the specific steps and parameters described previously (Shen et al ., ).…”

Section: Methodsmentioning

confidence: 97%

Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum)

Wen

Shen

et al. 2018

Plant Biotechnology Journal

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SummaryBrown fibre cotton is an environmental‐friendly resource that plays a key role in the textile industry. However, the fibre quality and yield of natural brown cotton are poor, and fundamental research on brown cotton is relatively scarce. To understand the genetic basis of brown fibre cotton, we constructed linkage and association populations to systematically examine brown fibre accessions. We fine‐mapped the brown fibre region, Lc 1, and dissected it into 2 loci, qBF‐A07‐1 and qBF‐A07‐2. The qBF‐A07‐1 locus mediates the initiation of brown fibre production, whereas the shade of the brown fibre is affected by the interaction between qBF‐A07‐1 and qBF‐A07‐2. Gh_A07G2341 and Gh_A07G0100 were identified as candidate genes for qBF‐A07‐1 and qBF‐A07‐2, respectively. Haploid analysis of the signals significantly associated with these two loci showed that most tetraploid modern brown cotton accessions exhibit the introgression signature of Gossypium barbadense. We identified 10 quantitative trait loci (QTLs) for fibre yield and 19 QTLs for fibre quality through a genome‐wide association study (GWAS) and found that qBF‐A07‐2 negatively affects fibre yield and quality through an epistatic interaction with qBF‐A07‐1. This study sheds light on the genetics of fibre colour and lint‐related traits in brown fibre cotton, which will guide the elite cultivars breeding of brown fibre cotton.

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“…Additionally, it does not necessarily require full genomes sequences or genome SNPs [ 32 ]. In cotton, few reports of SLAF-seq are available regarding the construction of high-density genetic maps [ 36 ], identification of favorable alleles and candidate genes [ 37 ], or comprehensive analysis of polymorphisms among tetraploid cotton species [ 38 ]. In this study, a SLAF-seq strategy was used in the ILs population in order to identify QTLs for fiber quality and yield from wild relative species.…”

Section: Discussionmentioning

confidence: 99%

QTL Mapping for Fiber Quality and Yield Traits Based on Introgression Lines Derived from Gossypium hirsutum × G. tomentosum

Keerio

Shen

Nie

et al. 2018

IJMS

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The tetraploid species Gossypium hirsutum is cultivated widely throughout the world with high yield and moderate fiber quality, but its genetic basis is narrow. A set of 107 introgression lines (ILs) was developed with an interspecific cross using G. hirsutum acc. 4105 as the recurrent parent and G. tomentosum as the donor parent. A specific locus amplified fragment sequencing (SLAF-seq) strategy was used to obtain high-throughput single nucleotide polymorphism (SNP) markers. In total, 3157 high-quality SNP markers were obtained and further used for identification of quantitative trait loci (QTLs) for fiber quality and yield traits evaluated in multiple environments. In total, 74 QTLs were detected that were associated with five fiber quality traits (30 QTLs) and eight yield traits (44 QTLs), with 2.02–30.15% of the phenotypic variance explained (PVE), and 69 markers were found to be associated with these thirteen traits. Eleven chromosomes in the A sub-genome (At) harbored 47 QTLs, and nine chromosomes in the D sub-genome (Dt) harbored 27 QTLs. More than half (44 QTLs = 59.45%) showed positive additive effects for fiber and yield traits. Five QTL clusters were identified, with three in the At, comprised of thirteen QTLs, and two in the Dt comprised of seven QTLs. The ILs developed in this study and the identified QTLs will facilitate further molecular breeding for improvement of Upland cotton in terms of higher yield with enhanced fiber quality.

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Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq

Cited by 31 publications

References 55 publications

Genome Resequencing Reveals Genetic Variation between the Parents of An Elite Hybrid Upland Cotton

Genome Resequencing Reveals Genetic Variation between the Parents of An Elite Hybrid Upland Cotton

Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum)

QTL Mapping for Fiber Quality and Yield Traits Based on Introgression Lines Derived from Gossypium hirsutum × G. tomentosum

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