Relationship of Cultivated Grain Amaranth Species and Wild Relative Accessions

Abstract

Amaranthus is a genus of C4 dicotyledonous herbaceous plants, and three New World species have been domesticated to produce grain crops with light colored seed which are classified as pseudo-cereals rich in protein and minerals. A core collection of grain amaranths and immediate precursor species has been established, representing the closest related species. The goal of this study was to evaluate the genetic diversity in that collection of cultivated and wild species, using competitive allele single nucleotide polymorphism markers. A secondary objective was to determine the relationships among the three cultivated species and non-domesticated Amaranthus, while a third objective was to evaluate the utility of the markers in detecting diversity in the 276 genotypes. The markers were found to be highly variable with an average polymorphism information content of 0.365. All markers were bi-allelic; and the major allele frequency ranged from 0.388 to 0.871. Population structure analysis of the cultigens revealed the presence of two sub populations. Phylogeny confirmed that the two Mesoamerican species, Amaranthus cruentus and Amaranthus hypochondriacus, were related and distant from the South American species Amaranthus caudatus, which in turn was very closely clustered with Amaranthus quitensis, even though this is considered a weedy relative. The first pair of species were likely to have inter-crossed, while the latter two likely exist in a wild-cultivated hybrid state. In conclusion, the results of this SNP study provided insights on amaranth cultivars and their relationship to wild species, the probable domestication events leading to the cultivars, and possible crop breeding or germplasm conservation strategies.

Evolutionary Genetics of Crop-Wild Complexes

“…Additionally, 'big data' and OA-RN will enable to unlock more efficiently variation hidden at crop wild complexes with nutritional value (e.g., Phaseolus bean species [15]), and those with a more industrial perspective (e.g., field cress, a promising oil crop for the subarctic [14]). Based on this compilation, we encourage oncoming studies to: (1) explicitly test evolutionary scenarios concerning the domestication of the ancient grain amaranth via approximate Bayesian computation (ABC) demographic inferences [13] and ML [19,20], (2) narrow the genetic mapping of key domestication-related traits in the modern breeding of field cress [14] via genomewide association studies (GWAS) and GP [18], and (3) utilize tepary bean as a source of adapted alleles for drought tolerance (and potentially heat tolerance) in common bean [15] via inter-specific crossing schemes [21] and more modern GABC-based indirect introgression breeding.…”

“…Data Availability Statement: For original datasets, please refer to the published articles [13][14][15][16][17] within the Special Issue "Evolutionary Genetics of Plant Crop-Wild Complexes: From Fundamental to Applied Research" (https://www.mdpi.com/journal/genes/special_issues/Plant_Crop_Wild).…”

“…In an effort to unveil the domestication of an ancient grain ( Figure 1 ), Thapa et al [ 13 ] studied the relationship of cultivated grain amaranth species and their wild relatives across a diverse panel of 276 accessions using Kompetitive Allele Specific PCR (KASP)-based single nucleotide polymorphism (SNP) markers. The authors interpreted potential domestication events.…”

“…The pillars of such discussion include the need to: (1) monitor and forecast gender and generation gaps to shrink disparity over time, (2) fund long-term synergies to leverage plant resources independent of market trends [ 45 ], (3) bridge plant germplasm resources with plant breeding [ 46 ], and (4) encourage joint training programs in last-generation technologies to speed up breeding cycles [ 18 ] and mitigate tradeoffs [ 47 ]. In parallel, it is necessary to find innovative bio-economical uses (such as was carried out by Hammenhag et al [ 14 ]), and to (5) harness neglected or underutilized species [ 48 ] as a source of new [ 49 ] and future [ 37 ] crops (as envisioned by Buitrago-Bitar et al [ 15 ] and Thapa et al [ 13 ]). We look forward to seeing future research implementing these recommendations on crop–wild complexes [ 50 , 51 , 52 , 53 ].…”

“…Therefore, the goal of this Special Issue was to summarize fundamental and applied approaches on the evolutionary genetics in crop species and their CWR. Specifically, this compilation offers new insights into: (1) the evolutionary genetics of CWR [ 13 ] and the genomic consequences of domestication [ 14 ], (2) the role of crop–wild gene flow in adaptation [ 15 ], the utility to breed wild resources for climate change [ 16 ], and the necessity to consolidate open-source scientific networks [ 17 ] targeting underutilized/understudied plant resources.…”