A multiple phenotype imputation method for genetic diversity and core collection in Taiwanese vegetable soybean

Abstract

Establishment of vegetable soybean (edamame) [Glycine max (L.) Merr.] germplasms has been highly valued in Asia and the United States owing to the increasing market demand for edamame. The idea of core collection (CC) is to shorten the breeding program so as to improve the availability of germplasm resources. However, multidimensional phenotypes typically are highly correlated and have different levels of missing rate, often failing to capture the underlying pattern of germplasms and select CC precisely. These are commonly observed on correlated samples. To overcome such scenario, we introduced the “multiple imputation” (MI) method to iteratively impute missing phenotypes for 46 morphological traits and jointly analyzed high-dimensional imputed missing phenotypes (ECimpu) to explore population structure and relatedness among 200 Taiwanese vegetable soybean accessions. An advanced maximization strategy with a heuristic algorithm and PowerCore was used to evaluate the morphological diversity among the ECimpu. In total, 36 accessions (denoted as CCimpu) were efficiently selected representing high diversity and the entire coverage of the ECimpu. Only 4 (8.7%) traits showed slightly significant differences between the CCimpu and ECimpu. Compared to the ECimpu, 96% traits retained all characteristics or had a slight diversity loss in the CCimpu. The CCimpu exhibited a small percentage of significant mean difference (4.51%), and large coincidence rate (98.1%), variable rate (138.76%), and coverage (close to 100%), indicating the representativeness of the ECimpu. We noted that the CCimpu outperformed the CCraw in evaluation properties, suggesting that the multiple phenotype imputation method has the potential to deal with missing phenotypes in correlated samples efficiently and reliably without re-phenotyping accessions. Our results illustrated a significant role of imputed missing phenotypes in support of the MI-based framework for plant-breeding programs.

RETRACTED: Genomic Footprints of Selection for Enhancing Productivity in Taiwanese Vegetable Soybeans through Core Collection Framework

“…Overall missing rates were 7.5% and 10.8% for grain and vegetable soybeans, categorized as missing completely at random or missing at random. Prior studies have shown that missing phenotypes can influence genetic distance calculations, potentially affecting core collection representativeness [2,14].…”

“…For instance, the vegetable soybean variety 'Ryokkoh' (Vegsoy_023) from Japan has been used as a parent genotype to Taiwan's breeding programs for decades. Noteworthy varieties such as 'Kaorihime' (Vegsoy_008), 'Blue Side' (Vegsoy_010), and 'Chakaori' (Vegsoy_043) have been recognized for their large seeds and abundance of aromatic components [2,41,42]. Moreover, the 192 grain soybeans from 29 countries worldwide constitute a diverse and highly heterogeneous pool (Fig.…”

“…Vegetable soybeans boast large seed sizes and are rich sources of plant proteins, carbohydrates, dietary fiber, vitamins, minerals, antioxidants, and isoflavones [1]. The rising awareness of healthy dietary pattern has driven the demand for vegetable soybeans across diverse geographic regions, including Asia, the Americas, Europe, and sub-Saharan Africa [2,3]. Soybeans were domesticated from wild soybeans (Glycine soja Sieb.…”

“…Additionally, the sampling strategy of germplasms should be expanded to encompass regions with distinct environmental conditions to capture the full spectrum of genetic diversity. The incorporation of the rich reservoirs of germplasm from Taiwan and Japan [2,3] would provide valuable insights into the population structure and genetic architecture of vegetable soybeans.…”

“…The National Plant Genetic Resources Center (NPGRC) at the Taiwan Agricultural Research Institute houses a broad collection of plant germplasms, comprising a diverse panel of soybean accessions sourced from domestic and exotic landraces and varieties. Within this collection, certain ancestors vegetable soybeans in Taiwan have been incorporated into breeding programs [2]. A notable example is the 'Ryokkoh' from Japan, a superior ancestor of vegetable soybean that has been used as a parent genotype for several decades.…”