An InDel-based linkage map of hot pepper (Capsicum annuum)

Li, Weipeng; Cheng, Jimin; Wu, Zhiming; Qin, Cheng; Tan, Suxu; Tang, Xin; Cui, Junjie; Zhang, Lili; Hu, Kailin

doi:10.1007/s11032-015-0219-3

Cited by 48 publications

(39 citation statements)

References 58 publications

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“…In addition, to our knowledge, InDel markers have seldom been used for genetic mapping in spite of more intensive sequencing of pepper in recent years [ 26 – 29 ]. Fairly recently, we constructed an initial InDel-based genetic map (BB-InDel map) using an intraspecific population [ 30 ].…”

Section: Introductionmentioning

confidence: 99%

Construction of an Interspecific Genetic Map Based on InDel and SSR for Mapping the QTLs Affecting the Initiation of Flower Primordia in Pepper (Capsicum spp.)

et al. 2015

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Re-sequencing permits the mining of genome-wide variations on a large scale and provides excellent resources for the research community. To accelerate the development and application of molecular markers and identify the QTLs affecting the flowering time-related trait in pepper, a total of 1,038 pairs of InDel and 674 SSR primers from different sources were used for genetic mapping using the F2 population (n = 154) derived from a cross between BA3 (C. annuum) and YNXML (C. frutescens). Of these, a total of 224 simple PCR-based markers, including 129 InDels and 95 SSRs, were validated and integrated into a map, which was designated as the BY map. The BY map consisted of 13 linkage groups (LGs) and spanned a total genetic distance of 1,249.77 cM with an average marker distance of 5.60 cM. Comparative analysis of the genetic and physical map based on the anchored markers showed that the BY map covered nearly the whole pepper genome. Based on the BY map, one major and five minor QTLs affecting the number of leaves on the primary axis (Nle) were detected on chromosomes P2, P7, P10 and P11 in 2012. The major QTL on P2 was confirmed based on another subset of the same F2 population (n = 147) in 2014 with selective genotyping of markers from the BY map. With the accomplishment of pepper whole genome sequencing and annotations (release 2.0), 153 candidate genes were predicted to embed in the Nle2.2 region, of which 12 important flowering related genes were obtained. The InDel/SSR-based interspecific genetic map, QTLs and candidate genes obtained by the present study will be useful for the downstream isolation of flowering time-related gene and other genetic applications for pepper.

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Section: Introductionmentioning

confidence: 99%

Construction of an Interspecific Genetic Map Based on InDel and SSR for Mapping the QTLs Affecting the Initiation of Flower Primordia in Pepper (Capsicum spp.)

et al. 2015

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“…The genome sequence of almond that we present in this paper will foster the knowledge on the genetics and breeding of this species by providing useful information on genes and markers with an unprecedented level of detail. For example, in addition to the variability for SNP markers that is described here, we found a high number of insertion/deletion variants of sizes >20 within almond and many more between almond and peach, that can be used as simple and cheap markers for genetic analysis as it has been done in other species (Wu et al 2013;Li et al 2015;Jain et al 2019). Prunus crops are unique in the sense of being an economically important group of species that share an essentially common genome (Aranzana et al 2019).…”

Section: Discussionmentioning

confidence: 66%

Transposons played a major role in the diversification between the closely related almond (Prunus dulcis) and peach (P. persica) genomes: Results from the almond genome sequence

Alioto

Alexiou

Bardil

et al. 2019

Preprint

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Combining both short and long-read sequencing, we have estimated the almond Prunus dulcis cv. Texas genome size in 235 Mbp and assembled 227.6 Mb of its sequence. The highly heterozygous compact genome of Texas comprises eight chromosomes, to which we have anchored over 91% of the assembly. We annotated 27,042 protein-coding genes and 6,800 non-coding transcripts. High levels of genetic variability were characterized after resequencing a collection of ten almond accessions. Phylogenomic comparison with the genomes of 16 other close and distant species allowed estimating that almond and peach diverged around 5.88 Mya. Comparison between peach and almond genomes confirmed the high synteny between these close relatives, but also revealed high numbers of presence-absence variants, many attributable to the movement of transposable elements (TEs). The number and distribution of TEs between peach and almond was similar, but the history of TE movement was distinct, with peach having a larger proportion of recent transpositions and almond preserving a higher level of polymorphism in the older TEs. When focusing on specific genes involved in key characters such as the bitter vs. sweet kernel taste and the formation of a fleshy mesocarp, we found that for one gene associated with the biosynthesis of amygdalin that confers the bitter kernel taste, several TEs were inserted in its vicinity only in sweet almond cultivars but not in bitter cultivars and Prunus bitter kernel relatives, including P. webbii, P. mume, and other species like peach and cherry. TE insertions likely to produce affects in the expression of six more genes involved in the formation of the fleshy mesocarp were also identified.Altogether, our results suggest a key role of TEs in the recent history and diversification of almond with respect to peach.3

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“…Recently, the genomes of two C. annuum cultivars, Zunla-1 and CM334, were sequenced [3,13], which provided an important platform for the detection and development of genome-wide simple sequence repeats (SSR) and insertion or deletion (InDel) markers [14][15][16]. Although a large number of SSR and InDel markers have become available, these technologies are not suitable for large scale germplasm characterization.…”

Section: Introductionmentioning

confidence: 99%

“…Until now, the genetic diversity of domesticated Capsicum species has primarily been investigated using SSR markers [25][26][27], and genetic maps have been constructed with SSRs and InDels based on inter-or intraspecific populations [15,16,28]. However, discovery efforts for genome-wide SNPs have lagged significantly behind those for SSRs and InDels, and studies on genetic diversity of pepper varieties are limited.…”

Section: Introductionmentioning

confidence: 99%

Genotyping pepper varieties using Target SNP-seq reveals that population structure clusters according to fruit shape

Du¹,

Yang²,

Chen³

et al. 2019

Preprint

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Background The widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; however, little research has characterized the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of single-nucleotide polymorphisms (SNPs) was created that consisted of 97 perfect SNPs, which were identified using re-sequencing data from 35 diverse C. annuum lines. Based on this panel, a Target SNP-seq was designed that combined the multiplex amplification of the perfect SNPs with Illumina sequencing to detect polymorphisms across 271 commercial pepper varieties. Results The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content (PIC), observed heterozygosity (Ho), expected heterozygosity (He), and minor allele frequency (MAF), which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape; blocky, long horn, short horn, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn, linear, and blocky-fruited populations. A set of 35 core SNPs were then used as KASPar markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis (PCA) and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and Fst statistics. Notably, two SNP loci, CaSNP118 and CaSNP053, which are located on chromosome 11 and 6 were significantly associated with fruit shape (p < 1.0 × 10 -4) Conclusions Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of the pepper varieties is significantly influenced by breeding programs focused on fruit shape.

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An InDel-based linkage map of hot pepper (Capsicum annuum)

Cited by 48 publications

References 58 publications

Construction of an Interspecific Genetic Map Based on InDel and SSR for Mapping the QTLs Affecting the Initiation of Flower Primordia in Pepper (Capsicum spp.)

Construction of an Interspecific Genetic Map Based on InDel and SSR for Mapping the QTLs Affecting the Initiation of Flower Primordia in Pepper (Capsicum spp.)

Transposons played a major role in the diversification between the closely related almond (Prunus dulcis) and peach (P. persica) genomes: Results from the almond genome sequence

Genotyping pepper varieties using Target SNP-seq reveals that population structure clusters according to fruit shape

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