Examinando por Materia "Single nucleotide polymorphisms (SNPs)"

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Genetic variation in KRTAP11.1 gene of Suri alpaca (Vicugna pacos) from Puno, Peru
(Kasetsart University, 2019-02-28) Gallegos, Roberto; Rodriguez, Jorge; Quiñones, Ivana; Delgado De la Flor, Irene; Huanca Mamani, Teodosio; De la Cruz Perez, Abigail; Espinoza, José R.
The objective of this study was to identify genetic single nucleotide polymorphisms (SNPs) in the coding region of the KRTAP11.1 gene from the Suri alpaca population from Puno, Peru. Genomic DNA (n = 119) was used to amplify the 636 bp fragment of the coding region from the KRTAP11.1 gene. The polymerase chain reaction products of the KRTAP11.1 gene were sequenced by both strands and polymorphism type SNPs were identified. All SNPs (n = 3) were in Hardy-Weinberg equilibrium and had a high level of genotypic linkage disequilibrium with the presence of two haplotypes. All genetic polymorphisms generate non-synonymous amino acids changes: SNP 110 T>G (Ser>Ala), SNP 363 T>G (Phe>Cys) and SNP 375 A>C (Tyr>Ser). The results indicated the presence of moderate genetic diversity in the coding region of the KRTAP11.1 gene from the Suri alpaca population.
Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)
(Springer Nature, 2016-10-28) Arbizu Berrocal, Carlos Irvin; Ellison, Shelby L.; Senalik, Douglas; Simon, Philipp W.; Spooner, David M.
Results: We used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30% missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10% with a total of 18,565 SNPs, and (ii) rate of missing data 30%, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco. Daucus carota subsp. maximus was discriminated, but neither it, nor subsp. gummifer (defined in a broad sense) are monophyletic. Conclusions: Our study suggests that (1) the morphotypes identified as D. carota subspecies gummifer (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades with some accessions of subsp. carota, can be distinguished from each other but only with poor morphological support, (3) D. carota subsp. capillifolius, well distinguished morphologically, is an apospecies relative to North African populations of D. carota subsp. carota, (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in Daucus