A rapid and reliable PCR-restriction fragment length polymorphism (RFLP) marker for the identification of Amaranthus cruentus species

Relationship of Cultivated Grain Amaranth Species and Wild Relative Accessions

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.

Discovery of SNPs and indel 11-bp of the myostatin gene and its association with the double-muscled phenotype in Belgian blue crossbred cattle

Determining double muscle based on the myostatin (MSTN) gene in Belgian blue (BB), Peranakan Ongole (PO) and BB × PO crossbred cattle is very important for crossbreeding programs. This study aimed to investigate single-nucleotide polymorphisms (SNPs) and 11-bp deletions in the coding region of the MSTN gene and their relationship with the double-muscled phenotype in BB × PO crossbred cattle. A total of 86 blood samples were collected from 28 individual BB, 43 individual PO, and 15 individual BB × PO crossbred cattle. SNPs and indel 11-bp variation in the coding region of the MSTN gene were found using the sequencing method, followed by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. The MSTN gene in the coding region was detected in four SNPs found in PO cattle and its crossbreed. However, the four SNPs could not differentiate normal and double-muscled phenotypes although they are polymorphic. Moreover, in this study, an 11-bp deletion in exon 3 of the MSTN gene in BB cattle was found. In this case, by applying the PCR-RFLP technique using the restriction enzyme NmuCI (Tsp45I) in indel 11-bp, the genotypes that were successfully observed were +/+, +/del.11, and del.11/del.11.

Diversity in Grain Amaranths and Relatives Distinguished by Genotyping by Sequencing (GBS)

The genotyping by sequencing (GBS) method has become a molecular marker technology of choice for many crop plants because of its simultaneous discovery and evaluation of a large number of single nucleotide polymorphisms (SNPs) and utility for germplasm characterization. Genome representation and complexity reduction are the basis for GBS fingerprinting and can vary by species based on genome size and other sequence characteristics. Grain amaranths are a set of three species that were domesticated in the New World to be high protein, pseudo-cereal grain crops. The goal of this research was to employ the GBS technique for diversity evaluation in grain amaranth accessions and close relatives from six Amaranthus species and determine genetic differences and similarities between groupings. A total of 10,668 SNPs were discovered in 94 amaranth accessions with ApeKI complexity reduction and 10X genome coverage Illumina sequencing. The majority of the SNPs were species specific with 4,568 and 3,082 for the two grain amaranths originating in Central America Amaranthus cruentus and A. hypochondriacus and 3,284 found amongst both A. caudatus, originally domesticated in South America, and its close relative, A. quitensis. The distance matrix based on shared alleles provided information on the close relationships of the two cultivated Central American species with each other and of the wild and cultivated South American species with each other, as distinguished from the outgroup with two wild species, A. powellii and A. retroflexus. The GBS data also distinguished admixture between each pair of species and the geographical origins and seed colors of the accessions. The SNPs we discovered here can be used for marker development for future amaranth study.