Genetic diversity analysis and core collection construction for Amaranthus tricolor germplasm based on genome-wide single-nucleotide polymorphisms

Hoshikawa, Ken; Lin, Ya‐Ping; Schafleitner, Roland; Shirasawa, Kenta; Isobe, Sachiko; Nguyen, Duc Chinh; Ohsawa, Ryo; Yoshioka, Yosuke

doi:10.1016/j.scienta.2022.111428

Cited by 14 publications

(11 citation statements)

References 69 publications

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“…Furthermore, the collection presented here complements a CC made for vegetable species of amaranths ( Amaranthus tricolor , for example) by Hoshikawa et al. (2023) .…”

Section: Discussionmentioning

confidence: 98%

“…Furthermore, the collection presented here complements a CC made for vegetable species of amaranths (Amaranthus tricolor, for example) by Hoshikawa et al (2023). However, a decision should be made for the grain CC whether to include wild species A. hybridus and A. quitensis, as these tend to be hard to evaluate for yield traits, having smaller dark seeds and shattering before maturity.…”

Section: Discussionmentioning

confidence: 99%

“…The South American species was domesticated near the equator and is much more photoperiod sensitive than the North American species, which from here on in we will refer to as Mesoamerican. Conservation of grain amaranths falls primarily to national programs in the centers of origin, followed by the USDA collection (Ames, Iowa) and finally a subset of the mostly vegetable-type collection in WorldVeg ( Hoshikawa et al., 2023 ).…”

Section: Introductionmentioning

confidence: 99%

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Differentiation of Andean and Mesoamerican accessions in a proposed core collection of grain amaranths

et al. 2023

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Grain amaranths are made up of three New World species of pseudo-cereals with C4 photosynthesis from the dicotyledonous family Amaranthaceae and the genus Amaranthus. They originate in two ecoregions of the Americas, namely, the inter-Andean valleys of South America and the volcanic axis and lowlands of Mexico and Central America. These correspond to two centers of domestications for Andean and Mesoamerican crops, with one cultivated species found in the first region and two found in the latter region. To date, no core collection has been made for the grain amaranths in the United States Department of Agriculture (USDA) germplasm system. In this study, our objective was to create a core for the 2,899 gene bank accessions with collection site data by town or farm site of which 1,090 have current geo-referencing of latitude and longitude coordinates. We constituted the core with 260 genotypes of Amaranthus, which we evaluated with 90 single-nucleotide polymorphism markers. Our goal was to distinguish between Andean and Mesoamerican gene pools of amaranths, including the cultivated species and three possible progenitor or wild relative ancestors along with two more species in an outgroup. Population structure, clustering, and discriminant analysis for principal components showed that Andean species Amaranthus caudatus and Amaranthus quitensis shared fewer alleles with Mesoamerican species Amaranthus cruentus and Amaranthus hypochondriacus, compared to each group individually. Amaranthus hybridus was a bridge species that shared alleles with both regions. Molecular markers have the advantage over morphological traits at quickly distinguishing the Andean and Mesoamerican cultivars and have the added benefit of being useful for following inter-species crosses and introgression.

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“…Furthermore, the collection presented here complements a CC made for vegetable species of amaranths ( Amaranthus tricolor , for example) by Hoshikawa et al. (2023) .…”

Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Differentiation of Andean and Mesoamerican accessions in a proposed core collection of grain amaranths

et al. 2023

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“…Methods (3,4,5,6,7) were implemented in Core Hunter 3.0 [19]. Methods (7,8) were executed in the CoreSet of PowerMarker v3.25 [16].…”

Section: Construction Of Core Collectionsmentioning

confidence: 99%

“…All countries in the world attach great importance to the investigation, collection, evaluation, preservation, and utilization of germplasms [1]. However, the management and use of large germplasms is associated with a high economic cost to complete daily tasks, such as preservation, regeneration, reproduction, recording, and evaluation [2][3][4]. Therefore, the concept of a core set was introduced to help make these decisions.…”

Section: Introductionmentioning

confidence: 99%

Construction of a Core Collection of Germplasms from Chinese Fir Seed Orchards

Duan

Wang

et al. 2023

Forests

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Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is one of the most important tree species for afforestation in China. First-, second-, and third-generation seed orchards of Chinese fir have been established successively, and rich germplasms have been accumulated in the process of genetic improvement. It is necessary to build a core collection of germplasms from Chinese fir seed orchards. In this work, we constructed core collections representing the genetic diversity of Chinese fir seed orchard resources based on SSR data. A total of 607 seed orchard materials from three generations were used to determine the best sampling method and intensity by comparing and analyzing nine methods for constructing core collections. Core Hunter’s multi-strategy optimizes allele coverage and the distance criterion under a 30% sampling intensity (weight: A–NE, 0.7; CV, 0.3 and E–NE, 0.5; CV, 0.5), which is superior to other strategies and was selected as the best method. The two core collections (A–NE&CV73, E–NE&CV55) constructed contained all the alleles of the whole collection and effectively limited the homology in the core collections; each core collection contained 182 accessions. Our findings could contribute greatly towards improving the management of genetic resources in Chinese fir seed orchards and provide elite materials for future studies.

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