Article
Biochemistry & Molecular Biology
Limei Zhong, Youlin Zhu, Kenneth M. Olsen
Summary: This study used genome scans to uncover selection marks of hard and soft sweeps in domesticated soybeans, revealing that hard sweeps are mainly present in domesticated soybeans, while soft sweeps are more common in wild ancestors. The results contribute to a better understanding of genetic characteristics of domestication traits in soybeans.
Article
Plant Sciences
Yunsheng Wang, Andrew H. Paterson
Summary: This study re-sequenced and analyzed whole genome data from wild and cultivated Eriobotrya japonica, revealing a two-staged domestication process and enriching knowledge of crop domestication. Cultivated E. japonica showed little reduction in genome-wide nucleotide polymorphism compared with wild forms, and genes responsible for sugar biosynthesis were found to be enriched in regions harboring selective sweeps. An approach based on co-clustering into gene families and evaluating chromosome colinearity of orthologous and paralogous genes identified convergent/parallel selective sweeps among different crops.
Article
Agriculture, Dairy & Animal Science
Mohamad Ballan, Samuele Bovo, Francesca Bertolini, Giuseppina Schiavo, Michele Schiavitto, Riccardo Negrini, Luca Fontanesi
Summary: In this study, genotyping and analysis revealed the genetic relationship between exterior traits and rabbit breeds. It was found that breeds with similar phenotypic traits shared common ancestries and specific genes associated with coat color and body size were identified. This study provides insights into the genetic events that led to the formation of rabbit breeds and the genetic mechanisms behind their phenotypic variability.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2023)
Article
Genetics & Heredity
Antoine Moinet, Flavia Schlichta, Stephan Peischl, Laurent Excoffier
Summary: This article investigates the shape of neutral valleys of diversity under a model of population size change and compares it to signals of a selective sweep. The results show that selective sweep valleys of diversity are wider than neutral valleys, but it is possible to find a neutral valley with the same width as a given selective valley by parameterizing the model.
Article
Multidisciplinary Sciences
Alessandro Alves-Pereira, Maria Imaculada Zucchi, Charles R. Clement, Joao Paulo Gomes Viana, Jose Baldin Pinheiro, Elizabeth Ann Veasey, Anete Pereira de Souza
Summary: This study evaluated the genetic diversity of traditional manioc varieties conserved in a gene bank in Brazil. The researchers found that domestication and cultivation of manioc in different environments led to variations in selective signatures, and different biomes showed high levels of neutral genetic diversity within varieties.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Penghao Wang, Gaofeng Zhou, Jianbo Jian, Huaan Yang, Daniel Renshaw, Matthew K. Aubert, Jonathan Clements, Tianhua He, Mark Sweetingham, Chengdao Li
Summary: Shifting from a livestock-based protein diet to a plant-based protein diet is essential for global food sustainability, requiring increased production of protein-rich crops. The domestication of narrow-leafed lupin has led to the identification of key genetic loci and evidence of a domestication bottleneck. Genomic analysis provides insights into enhancing crop plant diversity for food security and sustainable agriculture.
Article
Plant Sciences
Yuting Ma, Wenyan Yang, Hongwei Zhang, Pingxi Wang, Qian Liu, Fenghai Li, Wanli Du
Summary: This research significantly advances our understanding of critical environmental factors influencing maize adaptation while simultaneously provides an invaluable gene resource for the development of climate-resilient maize hybrid varieties.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Xia Chen, Xue Bai, Huagui Liu, Binbin Zhao, Zhixun Yan, Yali Hou, Qin Chu
Summary: Copy number variation (CNV) plays an important role in chicken domestication and breed shaping, affecting genes related to nervous system, sensory, and follicle development. Comparisons between domestic breeds and wild red jungle fowl (RJF) revealed significant differences in genes associated with nervous, immunity, and reproductive system development. Breed-specific CNVs identified valuable genes related to beard trait, melanin deposition, aggressiveness, and traits like high egg production and fast-growing. These candidate genes provide valuable resources for further studies on phenotypic variation and artificial breeding of chickens.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Thaina Cortez, Horacio Montenegro, Luiz L. Coutinho, Luciana C. A. Regitano, Sonia C. S. Andrade
Summary: Evolutionary history and intense selective pressures can lead to changes in the genome of species. The genomic evolution of Bos species, particularly the economically important Nelore cattle breed in Brazil, was investigated in this study. Positive selection was observed in genes related to transport protein cobalamin, glycolipid metabolism, and hormone signaling in Nelore and B. indicus. The high gene contraction rate and the association of rapidly evolving gene families with amino acid biosynthesis, reproductive, and immune system-related pathways demonstrate the relevance of these traits from a domestication perspective. This research provides insights into how the genome responds to artificial selection and highlights the importance of selective pressures on traits relevant for animal breeding.
Article
Genetics & Heredity
Amir Fallahshahroudi, Martin Johnsson, Enrico Sorato, S. J. Kumari A. Ubhayasekera, Jonas Bergquist, Jordi Altimiras, Per Jensen
Summary: The genetic variation in TSHR between red junglefowl and domestic chicken is reflected in differences in abundance, gene expression levels, hormone levels, sexual maturity, and behavior.
Article
Plant Sciences
Dayong Wei, Nan Li, Nan Zhang, Feng Liu, Jie Wu, Sa Zhao, Jinjuan Shen, Zhimin Wang, Lisha Peng, Yonghong Fan, Jiaqin Mei, Qinglin Tang
Summary: The study investigates the impact of positively and negatively selected genes on the gene feature and function differentiation of Brassica tetraploids. The results show that PSGs are enriched in pathways related to environmental adaptation and reproduction, while NSGs are associated with various biological processes without clear evolutionary relationships. Additionally, the PSGs of B. carinata are specifically enriched in lipid biosynthesis and metabolism, contributing to its domestication as an oil crop.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Jun Li, Yuhang Zhang, Ruirui Ma, Wenxuan Huang, Jingjing Hou, Chao Fang, Lingshuang Wang, Zhihui Yuan, Qun Sun, Xuehui Dong, Yufeng Hou, Ying Wang, Fanjiang Kong, Lianjun Sun
Summary: This study elucidates the origin of seed morphology and quality variation in soybean and identifies the genes associated with seed coat color and seed thickness as tightly linked. The variation in seed morphology and quality occurred earlier than the variation in seed coat color during soybean domestication, and these variations are related to seed oil content and glycolysis biosynthesis in soybean.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Biotechnology & Applied Microbiology
Ya-Mei Ding, Yu Cao, Wei-Ping Zhang, Jun Chen, Jie Liu, Pan Li, Susanne S. Renner, Da-Yong Zhang, Wei-Ning Bai
Summary: In this study, the demographic histories of Persian walnut and iron walnut were inferred using whole-genome resequencing data and population-genetic approaches. The results suggest that the two species diverged from each other approximately 0.85 million years ago, with unidirectional gene flow from Persian walnut to iron walnut. The study also found that introgression from Persian walnut played a role in the domestication of iron walnut.
Article
Biology
Ming-Shan Wang, Jin-Jin Zhang, Xing Guo, Ming Li, Rachel Meyer, Hidayat Ashari, Zhu-Qing Zheng, Sheng Wang, Min-Sheng Peng, Yu Jiang, Mukesh Thakur, Chatmongkon Suwannapoom, Ali Esmailizadeh, Nalini Yasoda Hirimuthugoda, Moch Syamsul Arifin Zein, Szilvia Kusza, Hamed Kharrati-Koopaee, Lin Zeng, Yun-Mei Wang, Ting-Ting Yin, Min-Min Yang, Ming-Li Li, Xue-Mei Lu, Emiliano Lasagna, Simone Ceccobelli, Humpita Gamaralalage Thilini Nisanka Gunwardana, Thilina Madusanka Senasig, Shao-Hong Feng, Hao Zhang, Abul Kashem Fazlul Haque Bhuiyan, Muhammad Sajjad Khan, Gamamada Liyanage Lalanie Pradeepa Silva, Le Thi Thuy, Okeyo A. Mwai, Mohamed Nawaz Mohamed Ibrahim, Guojie Zhang, Kai-Xing Qu, Olivier Hanotte, Beth Shapiro, Mirte Bosse, Dong-Dong Wu, Jian-Lin Han, Ya-Ping Zhang
Summary: Despite having higher genetic diversity, modern domestic chickens experienced a significant population size decline during early domestication compared to their wild counterparts. This led to an increase in deleterious mutations in chicken genomes, challenging modern breeding programs to effectively eliminate these genetic loads. Positive selection was found to decrease the incidence but increase the frequency of deleterious SNPs in domestic chicken genomes.
Article
Plant Sciences
Concetta Burgarella, Angelique Berger, Sylvain Glemin, Jacques David, Nancy Terrier, Monique Deu, David Pot
Summary: This study focused on Sorghum bicolor and utilized transcriptomic resources to explore the adaptive consequences of the domestication process. Gene expression and nucleotide variability analyses revealed downregulation and reduction of diversity in domesticated sorghum, with functional annotation pointing to metabolic pathways contributing to the sorghum domestication syndrome. The study identified significantly differentially expressed genes and highlighted large rewiring of the transcriptome during the domestication and improvement processes, paving the way for the identification of key domestication genes for breeding purposes.
FRONTIERS IN PLANT SCIENCE
(2021)