Limits...
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.).

Tan S, Cheng JW, Zhang L, Qin C, Nong DG, Li WP, Tang X, Wu ZM, Hu KL - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, South China Agricultural University, Guangzhou, China.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus

Likelihood profile comparison of single marker analysis with phenotypic data from 2012 and normalized, respectively.The threshold value of LOD = 2.5 was showed with green line.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4363154&req=5

pone.0119389.g003: Likelihood profile comparison of single marker analysis with phenotypic data from 2012 and normalized, respectively.The threshold value of LOD = 2.5 was showed with green line.

Mentions: To evaluate the QTL results, another subset of the F2 population (n = 147) was genotyped using a set of selective markers (n = 111) from the BY map and another map consisted of 13 LGs with 94 markers was constructed (unpublished data). After collecting the Nle phenotypic data from 139 out of 147 individuals planted in 2014, the major QTL, which was assumed to be equal to Nle2.2 since the LOD peak markers EMPS677 and CIDHjw2_2 were tightly linked with physical distance of ~882.07 kb, was repeatedly identified using either ICIM or CIM method (Table 4). The results showed that the effect of Nle2.2 on controlling the Nle was less affected by the environment and were consistent with the characterization of high heritability of this trait (Table 3). In addition, single marker analysis (SMA) was also carried out on a dataset that normalized from the phenotypic data of two years (2012 and 2014) with 21 selected positive markers (total number of the positive makers is 28) from the 2012 analyses. Plot of LOD (Fig. 3) showed that both peaks of 2012 and normalized were agreement with the results of ICIM and CIM indicating again that the environment has little influence on the Nle.


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.).

Tan S, Cheng JW, Zhang L, Qin C, Nong DG, Li WP, Tang X, Wu ZM, Hu KL - PLoS ONE (2015)

Likelihood profile comparison of single marker analysis with phenotypic data from 2012 and normalized, respectively.The threshold value of LOD = 2.5 was showed with green line.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4363154&req=5

pone.0119389.g003: Likelihood profile comparison of single marker analysis with phenotypic data from 2012 and normalized, respectively.The threshold value of LOD = 2.5 was showed with green line.
Mentions: To evaluate the QTL results, another subset of the F2 population (n = 147) was genotyped using a set of selective markers (n = 111) from the BY map and another map consisted of 13 LGs with 94 markers was constructed (unpublished data). After collecting the Nle phenotypic data from 139 out of 147 individuals planted in 2014, the major QTL, which was assumed to be equal to Nle2.2 since the LOD peak markers EMPS677 and CIDHjw2_2 were tightly linked with physical distance of ~882.07 kb, was repeatedly identified using either ICIM or CIM method (Table 4). The results showed that the effect of Nle2.2 on controlling the Nle was less affected by the environment and were consistent with the characterization of high heritability of this trait (Table 3). In addition, single marker analysis (SMA) was also carried out on a dataset that normalized from the phenotypic data of two years (2012 and 2014) with 21 selected positive markers (total number of the positive makers is 28) from the 2012 analyses. Plot of LOD (Fig. 3) showed that both peaks of 2012 and normalized were agreement with the results of ICIM and CIM indicating again that the environment has little influence on the Nle.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, South China Agricultural University, Guangzhou, China.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus