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Research Article

Comparative Genomic and Expression Analysis of MADS-box Gene family in Apple and Pear under Cold Stress

사과 및 배 MADS-box 유전자의 비교 유전체 분석 및 저온 스트레스 반응 특성 규명

Jun Seo Gi1†
,
Jun Hyeok Kim1†
,
Hye Jeong Cho1
,
Tae Yeong Lim1
,
Seungill Kim1*
길 준서1†
,
김 준혁1†
,
조 혜정1
,
임 태영1
,
김 승일1*
1Department of Environmental Horticulture, University of Seoul, Seoul 02504, Korea
1서울시립대학교 환경원예학과
*Corresponding Author
†These authors contributed equally to this work.
31 December 2025. pp. 781-793
PDF XML Citation
Abstract

MADS-box genes encode transcription factors critical for plant development, flowering, and stress responses. We re-annotated MADS-box genes in apple (Malus domestica) and pear (Pyrus pyrifolia), two economically significant Rosaceae species, revealing 113 previously unannotated genes. Comparative genomic analyses with Arabidopsis and other species highlighted evolutionary divergence, with domain and motif analyses demonstrating stronger conservation in MIKC-type genes compared to the M type. Phylogenetic reconstruction traced lineage-specific expansions, while a CAFE analysis identified SOC1 as the most rapidly expanding subfamily in Pyrus pyrifolia, likely driven by whole-genome duplication events—a pattern consistent with recent synteny network studies in Rosaceae. Under cold stress, expression profiling in Pyrus pyrifolia revealed a significant downregulation of SOC1, suggesting its role in temperature-sensitive signaling pathways. A co-expression network analysis further implicated PPYR_MADS_102 and PPYR_MADS_56 as key candidates for cold resistance, potentially regulating dormancy or stress-responsive pathways. Our study provides a refined genomic resource for Rosaceae, elucidates the evolutionary dynamics of MADS-box subfamilies, and identifies functional targets for improving cold tolerance in horticultural species.

Keywords
Malus domestica
Pyrus pyrifolia
RNA-seq
TGFam-Finder
transcription factor

MADS-box 유전자는 식물 발달, 개화 및 스트레스 반응에 필수적인 전사인자를 암호화한다. 본 연구는 경제적으로 중요한 두 장미과 종인 사과(Malus domestica)와 배(Pyrus pyrifolia)에서 MADS-box 유전자를 재동정하였으며, TGFam-Finder를 사용하여 이전에 동정되지 않았던 113개의 유전자를 발견했다. 애기장대(Arabidopsis) 및 다른 종들과의 비교 유전체 분석은 MADS-box 유전자의 진화적 분화를 보여주었으며, 도메인 및 모티프 분석 결과 M-type에 비해 MIKC-type 유전자에서 더 강한 보존성이 나타났다. 계통수 분석은 계통 특이적 확장을 추적하였고, CAFE 분석 결과 Pyrus pyrifolia에서 SOC1이 가장 빠르게 확장하는 subfamily임을 확인했다. 이는 전체 유전체 중복 사건에 의해 유도된 것으로 보이며, 장미과(Rosaceae)의 최근 유전자 배열 유사성(synteny) 네트워크 연구와 일치하는 패턴이다. 저온 스트레스 하에서 배(Pyrus pyrifolia)의 발현 프로파일 분석 결과, SOC1의 유의미한 발현 감소가 나타났으며, 이는 온도 감응성 신호 전달 경로에서 SOC1의 역할을 시사한다. 공동 발현 네트워크 분석은 PPYR_MADS_102와 PPYR_MADS_56이 저온 저항성의 주요 후보 유전자이며, 휴면 또는 스트레스 반응 경로를 조절할 가능성이 있음을 추가적으로 시사한다. 본 연구는 장미과 식물에 대한 정제된 유전체 자원을 제공하고, MADS-box subfamily의 진화적 동력을 밝히며, 원예 작물의 저온 내성을 개선하기 위한 기능적 표적 유전자를 제시한다.

키워드
Malus domestica
Pyrus pyrifolia
RNA-seq
TGFam-Finder
전사인자
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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 : 43
  • No :6
  • Pages :781-793
  • Received Date : 2025-04-09
  • Accepted Date : 2025-04-14
  • DOI :https://doi.org/10.7235/HORT.20250045
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