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2024 Vol.42, Issue 6 Preview Page

Research Article

Development of Gene-based Markers for capsanthin-capsorubin synthase and zeaxanthin epoxidase Genes to Distinguish Fruit Colors in Paprika (Capsicum annuum L.)

파프리카에서 과색 구분용 capsanthin-capsorubin synthase 및 zeaxanthin epoxidase 유전자 기반 분자표지 개발

Kang Min Lee1
,
Jong-Suk Park2
,
Ye-Ji Hong3
,
Jundae Lee14*
이 강민1
,
박 종숙2
,
홍 예지3
,
이 준대14*
1Department of Horticulture, Jeonbuk National University, Jeonju 54896, Korea
2Department of Horticulture, Jeollabuk-do Agricultural Research and Extension Services, Iksan 54591, Korea
3Fruit Vegetables Research Institute, Jeollabuk-do Agricultural Research and Extension Services, Gunsan 54062, Korea
4Institute of Agricultural Science and Technology, Jeonbuk National University, Jeonju 54896, Korea
1전북대학교 농업생명과학대학 원예학과
2전라북도농업기술원 원예과
3전라북도농업기술원 과채류연구소
4전북대학교 농업과학기술연구소
*Corresponding Author
31 December 2024. pp. 759-770
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Abstract

The fruit color of paprika (Capsicum annuum L.) is one of the main traits influencing consumers. Paprika fruit colors include red, yellow, and orange based on the different carotenoid contents. In this study, we aimed to develop gene-based markers to distinguish among three fruit colors, in this case red, yellow, and orange, by identifying genetic variations among the carotenoid biosynthesis genes in paprika. Four candidate genes, phytoene synthase (PSY), β-carotene hydroxylase (BCH), zeaxanthin epoxidase (ZEP), and capsanthin-capsorubin synthase (CCS), were selected, and the gene sequences were obtained from the NCBI database. The genes were sequenced and the genetic variations were uncovered using four red (KNMR, 19BR201, Sirocco, and GINA), three yellow (KNMY, Volante, and Romance Gold), and three orange (KNMOR, DSP7054, and ARO-50R) cultivars. Gene variations depending on the fruit color were detected in CCS and ZEP genes. Red paprika fruits contained the normal CCS gene (Ccs allele), while yellow and orange paprika fruits contained the non-functional deleted CCS gene (ccs allele). One base substitution was found in the ZEP gene. Yellow paprika fruits contained the A base of the SNP (functional Zep allele), while orange paprika fruits contained the G base of the SNP (non-functional zep allele). Red paprika fruits had the A or G base of the SNP. Two codominant high-resolution melting (HRM) markers, CCS-indel-HRM and ZEP1.2-SNP-HRM, were developed using the detected genetic variations of a large indel and a SNP, respectively. The markers were tested in 44 F1 cultivars, 31 inbred lines, two F2 populations consisting of 31 and 79 individuals, and 380 germplasms. It was found that red paprika fruits had the Ccs/Ccs or Ccs/ccs genotype regardless of the ZEP genotype, while yellow paprika fruits had the ccs/ccs and Zep/_ genotypes and orange paprika fruits had the ccs/ccs and zep/zep genotypes. The fruit color predictions with the markers were perfectly matched with the fruit color phenotypes, indicating that these markers can be useful for developing new red, yellow, or orange paprika varieties.

Keywords
carotenoid
CCS
HRM
indel
SNP
ZEP

파프리카에서 과색은 수요에 영향을 미치는 중요한 형질 중의 하나이다. 빨간색, 노란색, 주황색의 파프리카 과색은 다양한 카로티노이드의 축적되는 함량에 의해 결정된다. 본 연구에서는 카로티노이드 생합성 관련 유전자의 변이를 탐색하여 파프리카의 과색을 구분할 수 있는 분자표지를 개발하고자 하였다. 카로티노이드 생합성 유전자 중 후보 유전자로 phytoene synthase(PSY), β-carotene hydroxylase(BCH), zeaxanthin epoxidase(ZEP), capsanthin-capsorubin synthase(CCS) 유전자를 선발하여 NCBI 데이터베이스에서 유전자 서열을 확보하였다. 빨간색 파프리카 4개 품종(KNMR, 19BR201, Sirocco, GINA), 노란색 파프리카 3개 품종(KNMY, Volante, Romance Gold), 주황색 파프리카 3개 품종(KNMOR, DSP7054, ARO-50R)을 이용하여 각 유전자의 염기서열을 해독하였고 유전자 변이를 탐색하였다. 그 결과, CCS와 ZEP 유전자에서 유전변이를 탐색하였다. 빨간색 파프리카의 CCS 유전자는 정상(정상 Ccs 대립유전자)이었고, 노란색과 주황색 파프리카의 CCS 유전자에서 결실 부위를 가지고(돌연변이 ccs 대립유전자) 있었다. ZEP 유전자에서는 한 개의 SNP(A/G)를 확인하였는데, A 염기인 경우(정상 Zep 대립유전자)는 노란색이었고, G 염기인 경우(돌연변이 zep 대립유전자)는 주황색이었다. 빨간색 파프리카의 경우 A 또는 G 염기 다 나타났다. CCS 유전자의 결실 부위를 이용하여 CCS-indel-HRM 분자표지를 개발하였고, ZEP 유전자의 SNP를 이용하여 ZEP1.2-SNP-HRM 분자표지를 개발하였다. 분자표지의 적용성을 검정하기 위하여 다양한 파프리카 재료에 개발된 분자표지를 분석하였다. 그 결과 Ccs/Ccs 또는 Ccs/ccs 유전자형을 가질 경우 ZEP 유전자형이 어떤 것이든 상관없이 빨간색 파프리카로 나타났다. ccs/ccs 유전자형인 경우 노란색과 주황색이 나타났는데, ZEP 유전자에서 Zep/Zep 또는 Zep/zep 유전자형인 경우에는 노란색, zep/zep 유전자형인 경우에는 주황색으로 나타났다. 분자표지를 통하여 예측한 과색과 실제 과색 표현형이 완전히 일치하였기 때문에, 본 연구에서 개발된 분자표지는 향후 새로운 빨간색, 노란색, 주황색 파프리카 품종을 육성할 때 유용하게 사용될 수 있을 것으로 생각된다.

키워드
카로티노이드
캡산틴-캡소루빈 합성효소
HRM
삽입/결실
단염기다형성
제아잔틴 에폭시데이즈
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Information
  • Publisher :KOREAN SOCIETY FOR HORTICULTURAL SCIENCE
  • Publisher(Ko) :한국원예학회
  • Journal Title :Horticultural Science and Technology
  • Journal Title(Ko) :원예과학기술지
  • Volume : 42
  • No :6
  • Pages :759-770
  • Received Date : 2023-11-08
  • Revised Date : 2024-01-10
  • Accepted Date : 2024-01-10
  • DOI :https://doi.org/10.7235/HORT.20240052
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