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cacGMS: 특성평가 정보기반 식물 유전자원 군집 알고리즘
유동수(Dong Su Yu),강만정(Manjung Kang),노나영(Nayoung Ro),허온숙(Onsook Hur) 한국육종학회 2022 한국육종학회지 Vol.54 No.2
Plant germplasm is a part of living genetic resources, including seeds and plant materials, such as roots, leaves, and stems, and should be conserved and managed to maintain ecological biodiversity and to consistently generate the product and supply food crops. Plant germplasm can be categorized based on various genetic traits such as race, and clustering based on similar genetic traits is an efficient method for managing large numbers of germplasms. Therefore, we developed an algorithm, termed cacGMS (Clustering Analysis for Categorical genetic traits of germplasms in Genebank Management System), using categorical variables which statistically differentiate the datatype of genetic traits such as seed-coat color, seed shape, and flower color. Briefly, using Newman’s modularity method, cacGMS combines the hierarchical clustering algorithm using the Ward2 method and representative-based algorithms such as K-medoids, and it regroups all germplasms using germplasm core sets. We tested cacGMS using 2,378 pepper germplasms with 46 different categorical genetic traits, and it exhibited better performance than the hierarchical and K-medoids algorithms for the average distance among clusters (0.4534) and entropy (1.2672). Moreover, cacGMS showed better performance in terms of threshold (from 15 to 30) for genetic traits than other algorithms and provided similar results in a test run using tomato germplasm. From these results, we expect that cacGMS will be a useful tool for managing each group with numerous plant germplasms and facilitate the analysis of other studies, such as analysis of representative characteristics of clustered germplasms and of correlations among germplasms in a particular cluster.
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엽록체 유전정보를 이용한 두류 유전자원 형태적 형질의 유전력 분석
유동수,최유미,왕샤오한,강만정,Dong Su Yu,Yu-Mi Choi,Xiaohan Wang,Manjung Kang 한국자원식물학회 2023 한국자원식물학회지 Vol.36 No.4
Developing and breeding improved legume-based food resources require collecting useful genetic traits with heritability even though requiring some time-consuming, costly, and labor intensive. We attempted to infer heritability of nine genetic traits-days to flowering, days to maturity, period from flowering to maturity, the number of seeds per pod, 100-seeds weight, and four contents such as crude protein, crude oil, crude fiber, and dietary fiber-using 455 homologous chloroplast gene sets of six species of legumes. Correlation analysis between genetic trait differences and phylogenetic distance of homologous gene sets revealed that days to flowering, the number of seeds per pod, and crude oil content were influenced by genetic factors rather than environmental factors by 62.86%, 69.45%, 57.14% of correlated genes (P-value ≤ 0.05) and days to maturity showed intermediate genetic effects by 62.42% (P-value ≤ 0.1). The period from flowering to maturity and 100-seeds weight showed different results compared to those of some previous studies, which may be attributed to highly complicated internal (epistatic or additive gene effects) and external effects (cultural environment and human behaviors). Despite being slightly unexpected, our results and method can widely contribute to analyze heritability by including genetic information on mitochondria, nuclear genome, and single nucleotide polymorphisms.
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