QTLmapping for capsaicin and dihydrocapsaicin content in a population ofCapsicum annuum‘NB1’ × Capsicum chinense‘Bhut Jolokia’

Abstract

Capsaicinoids are pungent compounds used for industrial and medical purposes including food, medicine and cosmetics. The Indian local variety ‘Bhut Jolokia’ (Capsicum chinense Jacq.) is one of the world's hottest chilli peppers. It produces more than one million Scoville heat units (SHUs) in total capsaicinoids. In this study, our goal was to identify quantitative trait loci (QTLs) responsible for the high content of capsaicin and dihydrocapsaicin in ‘Bhut Jolokia’. Capsicum annuum ‘NB1’, a Korean pepper inbred line containing 14 000 SHUs, was used as a maternal line. An F2 population derived by crossing between ‘NB1’ and ‘Bhut Jolokia’ was generated to map QTLs for capsaicinoids content. A total of 234 markers, including 201 HRM, 21 SSR, 2 CAPS and 10 gene‐based markers of the capsaicinoid synthesis pathway, were mapped. The final map covered a total distance of 1175.2 cM and contained 12 linkage groups corresponding to the basic chromosome number of chilli pepper. Capsaicin and dihydrocapsaicin content were analysed in 175 F2 pepper fruits using the HPLC method. The maximum total capsaicinoids content was 1389 mg per 100g DW (dry weight), and the minimum content was 11 mg per 100g DW. Two QTLs (qcap3.1 and qcap6.1) for capsaicin content were identified on LG3 and LG6, and two QTLs (qhdc2.1 and qdhc2.2) for dihydrocapsaicin content were located on LG2. We did not detect QTLs for total capsaicinoids content. The QTL positions for capsaicin content were different from those for dihydrocapsaicin content. These results indicate that the complexity of selecting for more pungent chilli peppers must be considered in a chilli pepper breeding programme. The QTL‐linked markers identified here will be helpful to develop more pungent pepper varieties from ‘Bhut Jolokia’, a very hot pepper.

QTL mapping and GWAS reveal candidate genes controlling capsaicinoid content in Capsicum

“…Two QTLs from this study, one QTL from Lee et al . ()and one SNP from the GWAS were linked to CSE (Table ; Figure b). Even though the role of CSE in the capsaicinoid biosynthesis pathway is unknown, CSE is known to hydrolyse caffeoyl shikimate, which is an intermediate of phenylpropanoid pathway (Vanholme et al ., ).…”

“…In total, eight QTLs located on chromosomes 2, 3 and 6 were validated. A shared QTL on chromosome 3, which contains PD‐cap3 and TH‐total3.2 , was co‐located with qcap3.1 , which was previously identified in the F 2 population derived from a C. annuum ‘NB1’ × C. chinense ‘Bhut Jolokia’ cross (Lee et al ., ). TH‐total3.3 was also linked to cap3.1 and total3.1 detected in the C. annuum ‘NuMex Rnaky’ × C. frutescens ‘BG2814‐6’ F 2:3 population (Ben‐Chaim et al ., ).…”

“…Using the C. annuum ‘CM334’ reference genome, we compared the physical locations of capsaicinoid‐related QTLs detected in multiple analyses and capsaicinoid content‐associating SNPs from GWAS (Table S10). The QTLs from our research were also compared with those detected in other studies (Ben‐Chaim et al ., ; Blum et al ., ; Lee et al ., ; Nimmakayala et al ., ; Yarnes et al ., ). Before now, the comparison of QTLs from different studies was not feasible, due to the lack of a reference genome or common markers used for the genetic maps.…”

Natural variations in the MYB transcription factor MYB31 determine the evolution of extremely pungent peppers

“…Large‐scale QTL identification and genome‐wide association study (GWAS) strategies have been previously adopted to detect QTLs or genes associated with the control of variations in CAPD content among inter‐ and intraspecific varieties, and the detected QTLs varied among the populations used for analysis (Blum et al ., ; Ben‐Chaim et al ., ; Ogawa et al ., ; Nimmakayala et al ., ; Han et al ., ). Although the functions of AT3 , Kas , CoMT , AMT and CaMYB31 are related to CAPD biosynthesis (Stewart et al ., ; Abraham‐Juarez et al ., ; Gururaj et al ., ; Arce‐Rodríguez & Ochoa‐Alejo, ), only a few CAPD content‐related QTLs have been cloned and functionally verified based on fine mapping (Cheng et al ., ; Lee et al ., ; Nimmakayala et al ., ; Han et al ., ). Recently, recombinant inbred lines (RILs) and F 2 plants derived from a cross between the nonpungent C. annuum accession ‘YCM334’ and the pungent C. annuum cultivar ‘Tean’ were used to identify the nonpungency locus Pun3 on chromosome 7 (Han et al ., ).…”

“…The increased expression of CBGs is responsible for the elevated CAPD content (Aluru et al ., ; Sarpras et al ., ; Tanaka et al ., ). Some quantitative trait loci (QTLs) are responsible for the CAPD content variations between different Capsicum species (Blum et al ., ; Ben‐Chaim et al ., ; Lee et al ., ; Han et al ., ). However, the underlying genetic and molecular mechanisms associated with the evolution of the extreme pungency of C. chinense species remain elusive.…”