An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (<i>Capsicum annuum</i>)

Han, Koeun; Jeong, Hee-Jin; Yang, Heng; Kang, Sungmin; Kwon, Jae-Hoon; Kim, Seungill; Choi, Doil; Kang, Byoung−Cheorl

doi:10.1093/dnares/dsv038

Cited by 98 publications

(150 citation statements)

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“…Among them, five and 36 SNPs were also detected as being associated with capsaicin content, and only these reached the FDR threshold for this association. Several GWAS and QTL mapping studies have demonstrated that one locus can control multiple highly correlated traits (Bauchet et al ., ; Ben‐Chaim et al ., ; Crowell et al ., ; Han et al ., ; Wang et al ., ). We detected a high correlation between capsaicin, dihydrocapsaicin and total capsaicinoid contents; therefore, it is possible that some SNPs can affect these traits simultaneously.…”

Section: Discussionmentioning

confidence: 99%

“…Missing data for parents were imputed using the FSFHapImputation plugin for Tassel 5 (Swarts et al ., ), and the recombination breakpoints of the RILs were detected using a sliding window approach (Han et al ., ; Huang et al ., ). The ratio of SNPs with maternal and paternal genotypes was calculated for each window, defined as 18 linked SNPs, and the overall genotype of each window was decided.…”

Section: Methodsmentioning

confidence: 99%

“…The SNPs were more densely distributed at the ends of the chromosomes (Figure 2a). To correct for missing data and genotyping error, a sliding window approach was used (Han et al, 2016). Recombination breakpoints were determined using 18 consecutive SNPs as one sliding window, and a high-density bin map of the 'TH' RIL population was constructed.…”

Section: Bin Map Of Biparental Populationsmentioning

confidence: 99%

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QTLmapping andGWASreveal candidate genes controlling capsaicinoid content inCapsicum

Han

Lee

et al. 2018

Plant Biotechnology Journal

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SummaryCapsaicinoids are unique compounds produced only in peppers (Capsicum spp.). Several studies using classical quantitative trait loci (QTLs) mapping and genomewide association studies (GWAS) have identified QTLs controlling capsaicinoid content in peppers; however, neither the QTLs common to each population nor the candidate genes underlying them have been identified due to the limitations of each approach used. Here, we performed QTL mapping and GWAS for capsaicinoid content in peppers using two recombinant inbred line (RIL) populations and one GWAS population. Whole‐genome resequencing and genotyping by sequencing (GBS) were used to construct high‐density single nucleotide polymorphism (SNP) maps. Five QTL regions on chromosomes 1, 2, 3, 4 and 10 were commonly identified in both RIL populations over multiple locations and years. Furthermore, a total of 109 610 SNPs derived from two GBS libraries were used to analyse the GWAS population consisting of 208 C. annuum‐clade accessions. A total of 69 QTL regions were identified from the GWAS, 10 of which were co‐located with the QTLs identified from the two biparental populations. Within these regions, we were able to identify five candidate genes known to be involved in capsaicinoid biosynthesis. Our results demonstrate that QTL mapping and GBS‐GWAS represent a powerful combined approach for the identification of loci controlling complex traits.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Bin Map Of Biparental Populationsmentioning

confidence: 99%

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QTLmapping andGWASreveal candidate genes controlling capsaicinoid content inCapsicum

Han

Lee

et al. 2018

Plant Biotechnology Journal

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127

102

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“…A recent publication used a high‐density bin map that aligned to the same reference genome as our study (Han et al, 2016). Han et al (2016) and our study used intraspecific C. annuum RIL populations that aligned with the CM334 genome published in 2014 (Kim et al, 2014). Among 17 traits examined in both studies, fruit length, fruit diameter, and fruit color in the immature stage were the only common traits.…”

Section: Discussionmentioning

confidence: 99%

Quantitative Trait Loci Controlling Fruit Size and Other Horticultural Traits in Bell Pepper (Capsicum annuum)

et al. 2018

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Bell pepper ( L.) is a group of fruit vegetables that has large variation in fruit shape, fruit size, and horticultural traits. Using unadapted sources of germplasm to bring in novel alleles while maintaining favorable quality and horticultural traits is challenging for breeding in pepper. A genetic map with 318 loci from genotype-by-sequencing (GBS) and single nucleotide polymorphism assays was generated from a recombinant inbred line population derived from a cultivated bell-type 'Maor' and a landrace highly resistant to , 'Criollo de Morelos-334'. Forty-nine quantitative trait loci (QTLs) were detected for fruit, leaf, and horticultural traits with the scantwo permutation and stepwiseqtl methods from R/qtl. With the availability of a pepper reference genome and GBS data, candidate genes for pepper organ size and other horticultural traits were predicted. , , and genes were candidate genes for controlling organ sizes on chromosome 1, 2, and 3, respectively. Two candidate genes controlling trichome formation in pepper are located at chromosome 10: and . The locus on chromosome 10, which encodes a member of the R2R3 MYB-domain family of proteins, has a function in anthocyanin accumulation. These QTL results and the candidate genes for each trait emphasize the genetic basis of the important traits for breeding with unadapted parents in bell pepper.

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“…This pattern may be consistent with a QTL allele-such as one conferring a preferable freshuse phenotype-under selection in the Chile de Agua. Several loci on chromosome 6 are associated with fruit morphology (Han et al, 2016;Hill et al, 2017) including pericarp thickness (Rao, Chaim, Borovsky, & Paran, 2003), and flowering phenology traits (Yarnes et al, 2012), all of which might be under selective pressure in Chile de Agua. While such QTL could be potentially interesting candidates for follow-up research, a list of candidates from these data would be highly speculative and were thus not included.…”

Section: Signals Of Selection and Differentiation Across The Genomementioning

confidence: 99%

Genome‐wide genotyping of a novel Mexican Chile Pepper collection illuminates the history of landrace differentiation after Capsicum annuum L. domestication

Taitano

Bernau

Barbolla

et al. 2018

Evolutionary Applications

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Studies of genetic diversity among phenotypically distinct crop landraces improve our understanding of fruit evolution and genome structure under domestication. Chile peppers (Capsicum spp. L.) are economically valuable and culturally important species, and extensive phenotypic variation among landraces exists in southern Mexico, a center of C. annuum diversity. We collected 103 chile pepper seed accessions from 22 named landraces across 27 locations in southern Mexico. We genotyped these accessions with genotyping by sequencing (GBS), yielding 32,623 filtered single‐nucleotide polymorphisms. Afterward, we genotyped 32 additional C. annuum accessions from a global collection for comparison to the Mexican collection. Within the Mexican collection, genetic assignment analyses showed clear genetic differentiation between landraces and clarified the unique nature of the Tusta landrace. Further clustering analyses indicated that the largest fresh‐use Chile de Agua and dry‐use Costeño landraces were part of separate clades, indicating that these two landraces likely represent distinct populations. The global accessions showed considerable admixture and limited clustering, which may be due to the collapse of use‐type divisions outside of Central America. The separation of the Mexican landraces in part by fruit morphology related to use highlights the relevance of this use‐type morphological diversity for plant breeders and the utility of fruit development variation for evolutionary biologists.

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An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (Capsicum annuum)

Cited by 98 publications

References 33 publications

QTLmapping andGWASreveal candidate genes controlling capsaicinoid content inCapsicum

QTLmapping andGWASreveal candidate genes controlling capsaicinoid content inCapsicum

Quantitative Trait Loci Controlling Fruit Size and Other Horticultural Traits in Bell Pepper (Capsicum annuum)

Genome‐wide genotyping of a novel Mexican Chile Pepper collection illuminates the history of landrace differentiation after Capsicum annuum L. domestication

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