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

Li W, Cheng J, Wu Z, Qin C, Tan S, Tang X, Cui J, Zhang L, Hu K - Mol. Breed. (2015)

Bottom Line: Compared to the Zunla-1 reference physical map, high consistency was observed on all 12 chromosomes, and the total length of scaffold anchored and physical distance covered by this map was 299.66 and 2,558.68 Mb, respectively, which accounted for 8.95 and 76.38 % of the Zunla-1 reference genome (3.35 Gb), respectively.Furthermore, 37 scaffolds (total length of 36.21 Mb) from the pseudo-chromosome (P0) of the current genome assembly were newly assigned to the corresponding chromosomes by 40 InDel markers.Thus, this map provided good genome coverage and would be useful for basic and applied research in pepper.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, South China Agricultural University, Wushan Road 483, Guangzhou, 510642 Guangdong China.

ABSTRACT

Two independent pepper (Capsicum annuum) genomes were published recently, opening a new era of molecular genetics research on pepper. However, pepper molecular marker technologies are still mainly focusing on the simple sequence repeats derived from public database or genomic library. The development and application of the third generation marker system such as single nucleotide polymorphisms, structure variations as well as insertion/deletion polymorphisms (InDels) is still in its infancy. In the present study, we developed InDel markers for pepper genetic mapping with the convenience of two whole-genome re-sequenced inbred lines BA3 (C. annuum) and B702 (C. annuum). A total of 154,519 and 149,755 InDel (1-5 bp) sites were identified for BA3 and B702, respectively, by the alignment of re-sequencing reads to Zunla-1 reference genome. Then, 14,498 InDel sites (only 4 and 5 bp) that are different between BA3 and B702 were predicted. Finally, within a random set of 1,000 primer pairs, 251 InDel markers were validated and mapped onto a linkage map using F2 population derived from the intraspecific cross BA3 × B702. The first InDel-based map, named as BB-InDel map, consisted of 12 linkage groups, covered a genetic distance of 1,178.01 cM and the average distance between bin markers was 5.01 cM. Compared to the Zunla-1 reference physical map, high consistency was observed on all 12 chromosomes, and the total length of scaffold anchored and physical distance covered by this map was 299.66 and 2,558.68 Mb, respectively, which accounted for 8.95 and 76.38 % of the Zunla-1 reference genome (3.35 Gb), respectively. Furthermore, 37 scaffolds (total length of 36.21 Mb) from the pseudo-chromosome (P0) of the current genome assembly were newly assigned to the corresponding chromosomes by 40 InDel markers. Thus, this map provided good genome coverage and would be useful for basic and applied research in pepper.

No MeSH data available.


InDel-based linkage map of pepper (C. annuum) and comparison with its physical map. All InDel markers start with a prefix ‘CIDH’. Markers written with red color are anchored onto the pseudo-chromosome (P0) of the BB-SNP map-based reference genome assembly. A total of 31 distorted segregation markers mapped on this map are underlined and italic. (Color figure online)
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Fig1: InDel-based linkage map of pepper (C. annuum) and comparison with its physical map. All InDel markers start with a prefix ‘CIDH’. Markers written with red color are anchored onto the pseudo-chromosome (P0) of the BB-SNP map-based reference genome assembly. A total of 31 distorted segregation markers mapped on this map are underlined and italic. (Color figure online)

Mentions: The F2 population consisting of 178 progenies derived from the cross BA3 × B702 was genotyped with the above InDel markers with very less missing rate (<1.7 %). An intraspecific linkage map of C. annuum, designated as the BB-InDel map, was built with 251 InDel markers (236 genetic bins), and the remaining 21 markers could not be integrated because of insufficient linkage (Fig. 1). This is the first report on the construction of intraspecific linkage map purely based on InDel markers for pepper. In order to evaluate the transferability of InDel markers among C. annuum accessions, InDel frequency was calculated using the re-sequencing data from a set of C. annuum accessions. The mean frequency of 251 mapped InDels markers among the 17 C. annuum accessions was 20.07 % (Fig. 2), indicating that the BB-InDel map can be used for basic and applied research in the future.Fig. 1


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

Li W, Cheng J, Wu Z, Qin C, Tan S, Tang X, Cui J, Zhang L, Hu K - Mol. Breed. (2015)

InDel-based linkage map of pepper (C. annuum) and comparison with its physical map. All InDel markers start with a prefix ‘CIDH’. Markers written with red color are anchored onto the pseudo-chromosome (P0) of the BB-SNP map-based reference genome assembly. A total of 31 distorted segregation markers mapped on this map are underlined and italic. (Color figure online)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4300394&req=5

Fig1: InDel-based linkage map of pepper (C. annuum) and comparison with its physical map. All InDel markers start with a prefix ‘CIDH’. Markers written with red color are anchored onto the pseudo-chromosome (P0) of the BB-SNP map-based reference genome assembly. A total of 31 distorted segregation markers mapped on this map are underlined and italic. (Color figure online)
Mentions: The F2 population consisting of 178 progenies derived from the cross BA3 × B702 was genotyped with the above InDel markers with very less missing rate (<1.7 %). An intraspecific linkage map of C. annuum, designated as the BB-InDel map, was built with 251 InDel markers (236 genetic bins), and the remaining 21 markers could not be integrated because of insufficient linkage (Fig. 1). This is the first report on the construction of intraspecific linkage map purely based on InDel markers for pepper. In order to evaluate the transferability of InDel markers among C. annuum accessions, InDel frequency was calculated using the re-sequencing data from a set of C. annuum accessions. The mean frequency of 251 mapped InDels markers among the 17 C. annuum accessions was 20.07 % (Fig. 2), indicating that the BB-InDel map can be used for basic and applied research in the future.Fig. 1

Bottom Line: Compared to the Zunla-1 reference physical map, high consistency was observed on all 12 chromosomes, and the total length of scaffold anchored and physical distance covered by this map was 299.66 and 2,558.68 Mb, respectively, which accounted for 8.95 and 76.38 % of the Zunla-1 reference genome (3.35 Gb), respectively.Furthermore, 37 scaffolds (total length of 36.21 Mb) from the pseudo-chromosome (P0) of the current genome assembly were newly assigned to the corresponding chromosomes by 40 InDel markers.Thus, this map provided good genome coverage and would be useful for basic and applied research in pepper.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, South China Agricultural University, Wushan Road 483, Guangzhou, 510642 Guangdong China.

ABSTRACT

Two independent pepper (Capsicum annuum) genomes were published recently, opening a new era of molecular genetics research on pepper. However, pepper molecular marker technologies are still mainly focusing on the simple sequence repeats derived from public database or genomic library. The development and application of the third generation marker system such as single nucleotide polymorphisms, structure variations as well as insertion/deletion polymorphisms (InDels) is still in its infancy. In the present study, we developed InDel markers for pepper genetic mapping with the convenience of two whole-genome re-sequenced inbred lines BA3 (C. annuum) and B702 (C. annuum). A total of 154,519 and 149,755 InDel (1-5 bp) sites were identified for BA3 and B702, respectively, by the alignment of re-sequencing reads to Zunla-1 reference genome. Then, 14,498 InDel sites (only 4 and 5 bp) that are different between BA3 and B702 were predicted. Finally, within a random set of 1,000 primer pairs, 251 InDel markers were validated and mapped onto a linkage map using F2 population derived from the intraspecific cross BA3 × B702. The first InDel-based map, named as BB-InDel map, consisted of 12 linkage groups, covered a genetic distance of 1,178.01 cM and the average distance between bin markers was 5.01 cM. Compared to the Zunla-1 reference physical map, high consistency was observed on all 12 chromosomes, and the total length of scaffold anchored and physical distance covered by this map was 299.66 and 2,558.68 Mb, respectively, which accounted for 8.95 and 76.38 % of the Zunla-1 reference genome (3.35 Gb), respectively. Furthermore, 37 scaffolds (total length of 36.21 Mb) from the pseudo-chromosome (P0) of the current genome assembly were newly assigned to the corresponding chromosomes by 40 InDel markers. Thus, this map provided good genome coverage and would be useful for basic and applied research in pepper.

No MeSH data available.