• Title, Summary, Keyword: domestication

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Evolutionary dynamics of transposable elements during silkworm domestication

  • Han, Min-Jin;Xu, Hong-En;Xiong, Xiao-Min;Zhang, Hua-Hao
    • Genes and Genomics
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    • v.40 no.10
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    • pp.1041-1051
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    • 2018
  • Although there are some documented examples on population dynamics of transposable elements (TEs) in model organisms, the evolutionary dynamics of TEs in domesticated species has not been systematically investigated. The objective of this study is to understand population dynamics of TEs during silkworm domestication. In this work, using transposon-display we examined the polymorphism of seven TE families [they represent about 59% of silkworm (Bombyx mori) total TE content] in four domesticated silkworm populations and one wild silkworm population. Maximum likelihood (ML) was used to estimate selection pressure. Population differentiation and structure were performed by using AMOVA analysis and program DISTRUCT, respectively. The results of transposon-display showed that significant differentiation occurred between the domesticated silkworm and wild silkworm. These TEs have experienced expansions and fixation in the domesticated silkworm but not in wild silkworm. Furthermore, the ML results indicated that purifying selection of TEs in the domesticated silkworm were significantly weaker than that in the wild silkworm. Interestingly, an adaptation insertion induced by BmMITE-2 was found, and this insertion can reduce the polymorphism of the flanking regions of its neighboring COQ7 gene. Our results suggested that TEs expanded and were fixed in the domesticated silkworm might result from demographic effects and artificial selection during domestication. We concluded that the data presented in this study have general implication in animal and crop improvements as well as in domestication of new species.

Ethnobotany of Wild Baobab (Adansonia digitata L.): A Way Forward for Species Domestication and Conservation in Sudan

  • Gurashi, N.A.;Kordofani, M.A.Y.;Adam, Y.O.
    • Journal of Forest and Environmental Science
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    • v.33 no.4
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    • pp.270-280
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    • 2017
  • Selection of superior phenotypes of fruit trees and products based on established criteria by local people is a prerequisite for future species domestication and conservation. Thus the study objective was to identify the local people's perceptions and preferences on baobab trees and products. A sample of 142 respondents was randomly selected using structured interviews in Blue Nile and North Kordofan, Sudan in 2013. Descriptive analysis was employed using SPSS and Excel programs. The study results indicated that local people use the morphological characteristics of the tree (leaves, fruits, seeds, kernels and bark) to differentiate individual trees. Based on the perceptions, local people recorded trees with delicious leaves, white pulp color, big fruit size and mature capsule size, and high pulp yield as criteria for differentiating between baobab trees in the study areas. In contrast, the undesirable traits were connected to trees with acidic pulp, slimy pulp, bitter leaves, and low pulp yield. The study concluded that the ethnobotanical knowledge of the baobab tree and its products may play an important role in tree domestication and improvement in Sudan. However, further research on tree genetics is needed to complement the ethnobotanical knowledge for baobab resources domestication and conservation.

The domestication event of the Tibetan pig revealed to be in the upstream region of the Yellow River based on the mtDNA D-loop

  • Ge, Qianyun;Gao, Caixia;Cai, Yuan;Jiao, Ting;Quan, Jinqiang;Guo, Yongbo;Zheng, Wangshan;Zhao, Shengguo
    • Asian-Australasian Journal of Animal Sciences
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    • v.33 no.4
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    • pp.531-538
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    • 2020
  • Objective: Evidence from previous reports indicates that pig domestication in East Asia mainly occurred in the Mekong region and the middle and downstream regions of the Yangtze River. Further research identified two new origin centers for domestic pigs in the Tibetan Plateau and the islands of Southeast Asia. However, due to the small sample size of Tibetan pigs, details of the origin and spread of Tibetan pigs has not yet been established. Methods: We analyzed mitochondrial DNA control region (D-loop) variation in 1,201 individuals from nine Tibetan pig populations across five provinces. Comprehensive Tibetan pig samples were taken to perform the most detailed analysis of Tibetan pigs to date. Results: The result indicate that Rkaze pigs had the lowest level of diversity, while Changdu pigs had the highest diversity. Interestingly, these two populations were both in the Tibetan Plateau area. If we calculate diversity in terms of each province, the Tibetan Plateau area had the lowest diversity, while the Chinese province of Gansu had the highest diversity. Diversity gradient analysis of major haplotypes suggested three domestication centers of Tibetan pigs in the Tibetan Plateau and the Chinese provinces of Gansu and Yunnan. Conclusion: We found two new domestication centers for Tibetan pigs. One is in the Chinese province of Gansu, which lies in the upstream region of the Yellow River, and the other is in the Chinese province of Yunnan.

A Historical Study on the Utilization of Wild Vegetables as Foods in Korea (한국산채류 이용의 역사적 고찰)

  • LeeKim, Mie-Soon
    • Journal of the Korean Society of Food Culture
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    • v.1 no.2
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    • pp.167-170
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    • 1986
  • The first historical record on the use of wild edible plants as foods in Korea involves sswuk and manul concerned with the mythology of Tangun. Numerous names of wild vegetables had been recorded in various ancient books. Wild edible plants are of great value as food resources and for domestication, since they have variable edible portions and quite a long picking season. Several kinds of wild edible plants have been already grown as vegetable crops. Doragi (Platycodon grandiflorum) is probably the one with the longest history of cultivation. During World War II, an attempt had been made to substitute vegetable crops for wild edible plants. As picking wild greens requires a great deal of labor and plants of wild growth are limited in the amount, domestication of wild vegetables as crops appears to be an urgent need for securing food resources in Korea.

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The bovin phylogeny: A review

  • Sharma, Aditi;Lee, SeungHwan;Lee, JunHeon;Dang, Changgwon;Kim, Hyeong Cheul;Yeon, SeongHum;Kang, HeeSeol;Kanwar, Shamsher Singh;Vijh, Ramesh Kumar
    • Korean Journal of Agricultural Science
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    • v.41 no.4
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    • pp.405-413
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    • 2014
  • The evolutionary history of cattle and buffalo has always been a topic of great interest to the evolutionary biologists. The phylogenetic studies of bovin species has been carried out at various levels, varying from the study of domestication and migration of populations to major cladogenesis. Along with the archeological studies there are studies from molecular biology and more recently from genomics. The phylogenetic perspective of the bovins and their evolutionary history, are reviewed in terms of what has been done, what needs to be done and potential challenges in doing it.

In silico approaches to identify the functional and structural effects of non-synonymous SNPs in selective sweeps of the Berkshire pig genome

  • Shin, Donghyun;Oh, Jae-Don;Won, Kyeong-Hye;Song, Ki-Duk
    • Asian-Australasian Journal of Animal Sciences
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    • v.31 no.8
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    • pp.1150-1159
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    • 2018
  • Objective: Non-synonymous single nucleotide polymorphisms (nsSNPs) were identified in Berkshire selective sweep regions and then were investigated to discover genetic nsSNP mechanisms that were potentially associated with Berkshire domestication and meat quality. We further used bioinformatics tools to predict damaging amino-acid substitutions in Berkshire-related nsSNPs. Methods: nsSNPs were examined in whole genome resequencing data of 110 pigs, including 14 Berkshire pigs, generated using the Illumina Hiseq2000 platform to identify variations that might affect meat quality in Berkshire pigs. Results: Total 65,550 nsSNPs were identified in the mapped regions; among these, 319 were found in Berkshire selective-sweep regions reported in a previous study. Genes encompassing these nsSNPs were involved in lipid metabolism, intramuscular fatty-acid deposition, and muscle development. The effects of amino acid change by nsSNPs on protein functions were predicted using sorting intolerant from tolerant and polymorphism phenotyping V2 to reveal their potential roles in biological processes that may correlate with the unique Berkshire meat-quality traits. Conclusion: Our nsSNP findings confirmed the history of Berkshire pigs and illustrated the effects of domestication on generic-variation patterns. Our novel findings, which are generally consistent with those of previous studies, facilitated a better understanding of Berkshire domestication. In summary, we extensively investigated the relationship between genomic composition and phenotypic traits by scanning for nsSNPs in large-scale whole-genome sequencing data.

In silico approaches to discover the functional impact of non-synonymous single nucleotide polymorphisms in selective sweep regions of the Landrace genome

  • Shin, Donghyun;Won, Kyung-Hye;Song, Ki-Duk
    • Asian-Australasian Journal of Animal Sciences
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    • v.31 no.12
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    • pp.1980-1990
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    • 2018
  • Objective: The aim of this study was to discover the functional impact of non-synonymous single nucleotide polymorphisms (nsSNPs) that were found in selective sweep regions of the Landrace genome Methods: Whole-genome re-sequencing data were obtained from 40 pigs, including 14 Landrace, 16 Yorkshire, and 10 wild boars, which were generated with the Illumina HiSeq 2000 platform. The nsSNPs in the selective sweep regions of the Landrace genome were identified, and the impacts of these variations on protein function were predicted to reveal their potential association with traits of the Landrace breed, such as reproductive capacity. Results: Total of 53,998 nsSNPs in the mapped regions of pigs were identified, and among them, 345 nsSNPs were found in the selective sweep regions of the Landrace genome which were reported previously. The genes featuring these nsSNPs fell into various functional categories, such as reproductive capacity or growth and development during the perinatal period. The impacts of amino acid sequence changes by nsSNPs on protein function were predicted using two in silico SNP prediction algorithms, i.e., sorting intolerant from tolerant and polymorphism phenotyping v2, to reveal their potential roles in biological processes that might be associated with the reproductive capacity of the Landrace breed. Conclusion: The findings elucidated the domestication history of the Landrace breed and illustrated how Landrace domestication led to patterns of genetic variation related to superior reproductive capacity. Our novel findings will help understand the process of Landrace domestication at the genome level and provide SNPs that are informative for breeding.

Hanwoo cattle: origin, domestication, breeding strategies and genomic selection

  • Lee, Seung-Hwan;Park, Byoung-Ho;Sharma, Aditi;Dang, Chang-Gwon;Lee, Seung-Soo;Choi, Tae-Jeong;Choy, Yeon-Ho;Kim, Hyeong-Cheol;Jeon, Ki-Jun;Kim, Si-Dong;Yeon, Seong-Heum;Park, Soo-Bong;Kang, Hee-Seol
    • Journal of Animal Science and Technology
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    • v.56 no.1
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    • pp.2.1-2.8
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    • 2014
  • Hanwoo (Korean cattle) is the native, taurine type of cattle breed of Korea and its history as a draft animal dates back to 5000 Years. In earlier times Hanwoo was used extensively for farming, transportation. Over the period of time, Hanwoo has changed to be meat type cattle. Full-scale production of Hanwoo as meat-type cattle has occurred since 1960s with the rapid growth of the Korean economy. Hanwoo is one of the most economically important species in Korea as it is a significant source of nutrition to the Korean people. Hanwoo beef is the most cherished food of Korea. One of the main goals of researchers is to increase the meat quality, quantity and taste of the beef. In this review we describe the origin, domestication of Hanwoo cattle and breeding program initiated from 1980's. Moreover the advent of technological advancement had provided us a platform to perform genome wide selection on economic traits and its implementation into traditional breeding programs.

Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding

  • Zhang, Wei;Yang, Min;Wang, Yuanlang;Wu, Xudong;Zhang, Xiaodong;Ding, Yueyun;Yin, Zongjun
    • Asian-Australasian Journal of Animal Sciences
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    • v.33 no.5
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    • pp.712-721
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    • 2020
  • Objective: The Wannan Black pig is a typical Chinese indigenous, disease-resistant pig breed with high fertility, and a crude-feed tolerance that has been bred by artificial selection in the south of Anhui province for a long time. However, genome variation, genetic relationships with other pig breeds, and domestication, remain poorly understood. Here, we focus on elucidating the genetic characteristics of the Wannan Black pig and identifying selection signatures during domestication and breeding. Methods: We identified the whole-genome variation in the Wannan Black pig and performed population admixture analyses to determine genetic relationships with other domesticated pig breeds and wild boars. Then, we identified the selection signatures between the Wannan Black pig and Asian wild boars in 100-kb windows sliding in 10 kb steps by using two approaches: the fixation index (FST) and π ratios. Results: Resequencing the Wannan Black pig genome yielded 501.52 G of raw data. After calling single-nucleotide variants (SNVs) and insertions/deletions (InDels), we identified 21,316,754 SNVs and 5,067,206 InDels (2,898,582 inserts and 2,168,624 deletions). Additionally, we found genes associated with growth, immunity, and digestive functions. Conclusion: Our findings help in explaining the unique genetic and phenotypic characteristics of Wannan Black pigs, which in turn can be informative for future breeding programs of Wannan Black pigs.