Population structure

Diversity, population structure, and evolution of local peach cultivars in China identified by simple sequence repeats

Z. J. Shen, Ma, R. J., Cai, Z. X., Yu, M. L., and Zhang, Z., “Diversity, population structure, and evolution of local peach cultivars in China identified by simple sequence repeats”, vol. 14, pp. 101-117, 2015.

The fruit peach originated in China and has a history of domestication of more than 4000 years. Numerous local cultivars were selected during the long course of cultivation, and a great morphological diversity exists. To study the diversity and genetic background of local peach cultivars in China, a set of 158 accessions from different ecological regions, together with 27 modern varieties and 10 wild accessions, were evaluated using 49 simple sequence repeats (SSRs) covering the peach genome. Broad diversity was also observed in local cultivars at the SSR level.

A rapid screening of ancestry for genetic association studies in an admixed population from Pernambuco, Brazil

A. V. C. Coelho, Moura, R. R., Cavalcanti, C. A. J., Guimarães, R. L., Sandrin-Garcia, P., Crovella, S., and Brandão, L. A. C., “A rapid screening of ancestry for genetic association studies in an admixed population from Pernambuco, Brazil”, vol. 14, pp. 2876-2884, 2015.

Genetic association studies determine how genes influence traits. However, non-detected population substructure may bias the analysis, resulting in spurious results. One method to detect substructure is to genotype ancestry informative markers (AIMs) besides the candidate variants, quantifying how much ancestral populations contribute to the samples’ genetic background. The present study aimed to use a minimum quantity of markers, while retaining full potential to estimate ancestries.

Analysis of genetic diversity and trait correlations among Korean landrace rice (Oryza sativa L.)

F. P. Li, Lee, Y. S., Kwon, S. W., Li, G., and Park, Y. J., “Analysis of genetic diversity and trait correlations among Korean landrace rice (Oryza sativa L.)”, vol. 13, pp. 6316-6331, 2014.

This study analyzed 394 Korean rice landrace accessions, including 93 waxy varieties, for polymorphisms using 29 simple sequence repeat (SSR) markers. In total, 381 alleles served as raw data for estimating the genetic diversity (GD) and population structure. The number of alleles per locus ranged from 3 to 44 (average = 13.14). The expected heterozygosity and polymorphism information content (PIC) ranged from 0.0341 to 0.9358 (mean = 0.5623) and from 0.0783 to 0.9367 (mean = 0.5839), respectively.

Unraveling the variability and genetic structure of barker frog Physalaemus cuvieri (Leiuperinae) populations from different regions of Brazil

M. Conte, Targueta, C. P., Zucchi, M. I., Souza, A. P., and Recco-Pimentel, S. M., “Unraveling the variability and genetic structure of barker frog Physalaemus cuvieri (Leiuperinae) populations from different regions of Brazil”, vol. 13, pp. 8055-8065, 2014.

The barker frog Physalaemus cuvieri is widely distributed in South America and is found in all regions of Brazil. Significant intraspecific morphological variation in this species has been reported. To determine the genetic structure of the natural Brazilian populations of P. cuvieri, 10 different populations geographically separated by 99.41 to 2936.75 km were evaluated using 10 polymorphic microsatellite loci. In addition, mitochondrial DNA data were analyzed to determine genetic distance between the populations.

Population genetic structure of Aedes albopictus in Penang, Malaysia

M. K. N. Zawani, Abu, H. A., Sazaly, A. B., Zary, S. Y., and Darlina, M. N., “Population genetic structure of Aedes albopictus in Penang, Malaysia”, vol. 13, pp. 8184-8196, 2014.

The mosquito Aedes albopictus is indigenous to Southeast Asian and is a vector for arbovirus diseases. Studies examining the population genetics structure of A. albopictus have been conducted worldwide; however, there are no documented reports on the population genetic structure of A. albopictus in Malaysia, particularly in Penang. We examined the population genetics of A.

Genetic identification of Theobroma cacao L. trees with high Criollo ancestry in Soconusco, Chiapas, Mexico

J. A. Vázquez-Ovando, Molina-Freaner, F., Nuñez-Farfán, J., Ovando-Medina, I., and Salvador-Figueroa, M., “Genetic identification of Theobroma cacao L. trees with high Criollo ancestry in Soconusco, Chiapas, Mexico”, vol. 13, pp. 10404-10414, 2014.

Criollo-type cacao trees are an important pool of genes with potential to be used in cacao breeding and selection programs. For that reason, we assessed the diversity and population structure of Criollo-type trees (108 cultivars with Criollo phenotypic characteristics and 10 Criollo references) using 12 simple sequence repeat (SSR) markers. Cultivars were selected from 7 demes in the Soconusco region of southern Mexico. SSRs amplified 74 alleles with an average of 3.6 alleles per population.

Genetic diversity and population genetic structure of the miiuy croaker, Miichthys miiuy, in the East China Sea by microsatellite markers

Y. Qin, Sun, D. Q., Xu, T. J., Liu, X. Z., and Sun, Y. N., “Genetic diversity and population genetic structure of the miiuy croaker, Miichthys miiuy, in the East China Sea by microsatellite markers”, vol. 13, pp. 10600-10606, 2014.

Genetic diversity and patterns of population structure of the miiuy croaker were investigated using SSR markers. A set of 10 microsatellite loci revealed 40 alleles; the number of alleles varied from 2 to 10 for each marker. A relatively high level of genetic variability was observed between miiuy croaker individuals. Genetic diversity was relatively high within populations with corresponding high average gene flow. There were genealogical branches or clusters corresponding to sampling localities according to the UPGMA tree and principal component analysis.

Genetic structure and diversity analysis of the primary gene pool of chickpea using SSR markers

P. Choudhary, Khanna, S. M., Jain, P. K., Bharadwaj, C., Kumar, J., Lakhera, P. C., and Srinivasan, R., “Genetic structure and diversity analysis of the primary gene pool of chickpea using SSR markers”, vol. 11, pp. 891-905, 2012.

Members of the primary gene pool of the chickpea, including 38 accessions of Cicer arietinum, six of C. reticulatum and four of C. echinospermum grown in India were investigated using 100 SSR markers to analyze their genetic structure, diversity and relationships. We found considerable diversity, with a mean of 4.8 alleles per locus (ranging from 2 to 11); polymorphic information content ranged from 0.040 to 0.803, with a mean of 0.536.

Polymorphic microsatellite loci for Japanese Spanish mackerel (Scomberomorus niphonius)

L. Lin, Zhu, L., Liu, S. - F., Tang, Q. - S., Su, Y. - Q., and Zhuang, Z. - M., “Polymorphic microsatellite loci for Japanese Spanish mackerel (Scomberomorus niphonius)”, vol. 11. pp. 1205-1208, 2012.

We isolated and characterized 21 polymorphic microsatellite loci in Japanese Spanish mackerel (Scomberomorus niphonius) using a (GT)13-enriched genomic library. Forty individuals were collected from Qingdao, China. We found 3 to 24 alleles per locus, with a mean of 8.8. The observed and expected heterozygosities ranged from 0.263 to 0.975 and from 0.385 to 0.946, with means of 0.655 and 0.685, respectively. Deviation from Hardy-Weinberg proportions was detected at three loci. Two loci showed evidence for null alleles.

Molecular diversity and population structure of the forage grass Hemarthria compressa (Poaceae) in south China based on SRAP markers

L. - K. Huang, Zhang, X. - Q., Xie, W. - G., Zhang, J., Cheng, L., and Yan, H. D., “Molecular diversity and population structure of the forage grass Hemarthria compressa (Poaceae) in south China based on SRAP markers”, vol. 11, pp. 2441-2450, 2012.

Hemarthria compressa is one of the most important and widely utilized forage crops in south China, owing to its high forage yield and capability of adaptation to hot and humid conditions. We examined the population structure and genetic variation within and among 12 populations of H. compressa in south China using sequence-related amplified polymorphism (SRAP) markers. High genetic diversity was found in these samples [percentage polymorphic bands (PPB) = 82.21%, Shannon’s diversity index (I) = 0.352].

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