Article
Agriculture, Dairy & Animal Science
Yihao Zhi, Dandan Wang, Ke Zhang, Yangyang Wang, Wanzhuo Geng, Botong Chen, Hong Li, Zhuanjian Li, Yadong Tian, Xiangtao Kang, Xiaojun Liu
Summary: Using whole genome resequencing, this study investigated the genetic basis, genomic diversity, migration history, and selection factors of the indigenous chicken breeds in Henan Province, China. The results revealed close genetic relationships between Henan native chickens and neighboring provinces' chicken populations. Moreover, the study identified genes and biological processes related to body size, muscle development, reproduction, and aggression control in the unique phenotypes of Henan gamecocks. These findings provide valuable insights into the traits and potential utilization of Henan indigenous chickens.
Article
Agriculture, Dairy & Animal Science
Zhong Zhuang, Long Zhao, Weicheng Zong, Qixin Guo, Xiaofan Li, Yulin Bi, Zixiu Wang, Yong Jiang, Guohong Chen, Bichun Li, Guobin Chang, Hao Bai
Summary: South Asia and Southeast Asia are rich in poultry genetic resources, resulting in many unique local chicken breeds. However, with the rapid intensification of poultry farming worldwide, many local chicken breeds are threatened with extinction. It is imperative to strengthen the conservation and breeding of local chicken breeds in China and Vietnam.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
E. N. Nwachukwu, D. J. U. Kalla, H. O. Ukwu, C. C. Ogbu, J. Ezea, U. H. Udoh, O. O. Ekumankama
Summary: This study evaluated the genetic relatedness, diversity, and population structure of four indigenous cattle breeds in Nigeria. The results showed genetic differentiation among the breeds and suggested the potential for developing improved breeds through hybridization to enhance beef production and disease resistance.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2022)
Article
Agriculture, Dairy & Animal Science
M. Kanakachari, H. Rahman, R. N. Chatterjee, T. K. Bhattacharya
Summary: Native chickens in India play a significant role in the rural economy by providing additional income and nutritional security. This study comprehensively reviews the characteristics of Indian native chicken breeds and differentiates them from exotic breeds through phenotype, molecular parameters, and performance. The research reveals the genetic distance and unique position of Indian chickens in relation to exotic chickens, suggesting that breed signature has the potential to distinguish between the two populations.
WORLDS POULTRY SCIENCE JOURNAL
(2022)
Article
Agriculture, Dairy & Animal Science
H. D. Blackburn, B. C. Krehbiel
Summary: This study evaluated the genetic diversity of several traditional chicken breeds in the United States and aimed to provide baseline data for the conservation of their genetic resources. The results showed that there is significant genetic variability within these breeds' populations, and the gene bank has successfully captured this diversity for future use.
Article
Agriculture, Dairy & Animal Science
Peng Zhao, Li Zhang, Yin Liu, Zhengkun Wang, Hongyu Guo, Jun Li, Shuai Wu, Zefeng Gao, Hao Yuan
Summary: The objective of this study was to assess the genetic diversity, phylogenetic relationship, and population structure of five goat breeds in Shanxi, China. The results showed high genetic diversities in the five populations, with Licheng big green goat (LCBG) having the highest genetic diversity and Jinlan cashmere goat (JLCG) having the lowest genetic diversity. The genetic differentiation analysis revealed a close genetic relationship between LCBG and LLBG (Lvliang black goat), while JLCG showed the largest genetic distance from the other four populations. The population structure of JLCG differed from the other four populations. Understanding the genetic diversity and population structure of indigenous goats is crucial for genetic improvement, understanding environmental adaptation, and the utilization and conservation of goat breeds.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Dorcus Kholofelo Malomane, Steffen Weigend, Armin Otto Schmitt, Annett Weigend, Christian Reimer, Henner Simianer
Summary: Migration of a population from its founder population is expected to reduce genetic diversity and facilitate differentiation between populations, consistent with the theory of genetic isolation by distance. The genetic diversity of domesticated chicken populations is strongly correlated with their genetic distance to wild populations, and this relationship can predict the genetic diversity of domesticated populations. Genes with little genetic variation across populations, such as those associated with brain development, may be more conserved, while genes associated with processes like protein transport and metabolic processes may exhibit faster genetic diversity changes. Overall, these findings contribute to understanding the evolutionary patterns of different functional genomic regions in chicken.
GENETICS SELECTION EVOLUTION
(2021)
Article
Agriculture, Dairy & Animal Science
Karan Veer Singh, Ramendra Das, Monika Sodhi, R. S. Kataria
Summary: Characterization of the newly identified swamp buffalo population "Bhangor" from North East Indian using microsatellite markers revealed high genetic diversity and the absence of recent bottleneck.
ANIMAL BIOTECHNOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Yanka Mihailova, Krasimir Rusanov, Mila Rusanova, Pavlina Vassileva, Ivan Atanassov, Vasil Nikolov, Elena G. G. Todorovska
Summary: This study used microsatellite (SSR) markers to investigate the genetic status of 12 Bulgarian autochthonous sheep breeds. A total of 600 individuals from 50 flocks were analyzed, and 228 alleles were found. The results showed low differentiation between the breeds, with two breeds being the most distinct and the remaining breeds showing poor breed differentiation. Proper management strategies and breeding policies are needed to avoid intermixing of breeds and preserve breed purity.
Article
Multidisciplinary Sciences
Vandana Manomohan, Ramasamy Saravanan, Rudolf Pichler, Nagarajan Murali, Karuppusamy Sivakumar, Krovvidi Sudhakar, Raja K. Nachiappan, Kathiravan Periasamy
Summary: The study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. It reveals moderate genetic diversity in South Indian cattle, with distinct genetic structures among different breeds and taurine admixture in some breeds. The study suggests concerns regarding endangerment, inbreeding, lack of purebred bulls, and increasing levels of taurine admixture in zebu cattle in South India, emphasizing the importance of breeding strategies and conservation efforts.
Article
Agriculture, Dairy & Animal Science
Renata Klein, Janos Olah, Sandor Mihok, Janos Posta
Summary: "The most important purpose of animal conservation programs is to maintain genetic variability. The Furioso-North Star, Gidran, and Nonius are Hungarian horse breeds that are currently endangered due to a reduction in population size and genetic variability caused by changes in their roles and advancements in technology. This study aims to provide information about the current breeding population and support breeder associations in gene conservation efforts. The study found that these breeds experienced a significant bottleneck effect in their breeding history and had high levels of inbreeding resulting from previously fixed alleles. The effective population sizes suggest that there is no problem with maintaining these horse breeds."
Article
Agriculture, Multidisciplinary
Jie Wang, Qiu-xia Lei, Ding-guo Cao, Yan Zhou, Hai-xia Han, Wei Liu, Da-peng Li, Fu-wei Li, Jie Liu
Summary: There are many different chicken breeds around the world with varying features, serving as valuable resources. However, there is currently a lack of knowledge regarding the genetic determinants responsible for the traits and characteristics of these breeds. Understanding the genetic mechanisms that explain the variations among breeds can assist breeders in developing improved chicken breeds.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2023)
Article
Agriculture, Dairy & Animal Science
Xufang Ren, Zi Guan, Haiying Li, Junhui Wen, Xiurong Zhao, Gang Wang, Xinye Zhang, Huie Wang, Li Zhang, Fuqing Yu, Lujiang Qu
Summary: This study investigated the population genetic structure and admixture of 5 Chinese gamecock breeds and their admixture with 9 other indigenous Chinese chicken breeds. The results showed that different gamecock breeds were grouped into different clusters. Gene flow was observed between gamecocks and indigenous chickens. Ancestral component analysis revealed the important role of modern domestic chickens in the history of Chinese gamecock domestication and evolution.
Article
Multidisciplinary Sciences
Aicha Edith Soara, Essodina Talaki, Guiguigbaza-Kossigan Dayo, Isidore Houaga, Kokou Tona, Mohammed Bakkali
Summary: In this study, the genetic diversity and phylogenic relationships of indigenous guinea fowl in Togo were assessed. The results showed a high genetic diversity and low levels of inbreeding. The genetic distances between phenotypes were small, indicating a strong genetic similarity. These findings are important for the conservation and improvement of this poultry resource.
Article
Agriculture, Dairy & Animal Science
Ruiyi Lin, Jiaquan Li, Yue Yang, Yinhua Yang, Jimin Chen, Fanglu Zhao, Tianfang Xiao
Summary: This study conducted a genome-wide comparative analysis of four indigenous Chinese duck breeds from Fujian Province to understand their genetic diversity and population structure. The results showed clear genetic differences among the four breeds, with identified hotspots of autozygosity and candidate genes involved in various traits. These findings provide insights for conservation strategies and further improvement of the duck breeds.
Article
Agriculture, Dairy & Animal Science
Jeremie Vandenplas, Herwin Eding, Mario P. L. Calus
Summary: Genetic groups, known as unknown or phantom parent groups, are often used in dairy cattle genetic evaluations to account for selection that cannot be explained by known genetic relationships. The Quaas and Pollak transformation can be applied to include genetic groups in the pedigree, reducing memory burden and computational costs compared to fitting genetic groups as covariates.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Johannes Geibel, Christian Reimer, Torsten Pook, Steffen Weigend, Annett Weigend, Henner Simianer
Summary: This study proposes an alternative approach to mitigate SNP ascertainment bias by using information from a small set of sequenced individuals, without prior knowledge of the array design. Results showed that a reference panel with at least one individual per population can effectively correct ascertainment bias for estimates of genetic parameters.
Article
Multidisciplinary Sciences
Johannes Geibel, Christian Reimer, Steffen Weigend, Annett Weigend, Torsten Pook, Henner Simianer
Summary: The study found that chip-based SNP data lack globally rare variants compared to whole-genome re-sequencing data, and exhibit SNP ascertainment bias. Rare alleles decrease gradually during development, with a strong selection for common SNPs. Additionally, manual selection of SNPs may lead to an overestimation of expected heterozygosity.
Article
Physiology
Christin Habig, Annett Weigend, Ulrich Baulain, Stefanie Petow, Steffen Weigend
Summary: This study aimed to describe blood parameters associated with egg laying and bone metabolism in two contemporary purebred layer lines over the course of the pre-laying period, laying period, and daily egg laying cycle. Significant differences were observed between the two lines in terms of calcium, osteocalcin, 25(OH)D-3, and estradiol-17 beta levels, indicating variations in their ability to cope with calcium demands related to egg production.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Genetics & Heredity
Simon Jansen, Ulrich Baulain, Christin Habig, Faisal Ramzan, Jens Schauer, Armin Otto Schmitt, Armin Manfred Scholz, Ahmad Reza Sharifi, Annett Weigend, Steffen Weigend
Summary: This study identified potentially informative genes associated with bone strength and density in laying hens, with each gene having a relatively small effect but collectively playing a significant role in bone integrity. These genes are likely involved in critical metabolic pathways for bone stability.
Article
Multidisciplinary Sciences
Stefanie Altgilbers, Sabine Klein, Claudia Dierks, Steffen Weigend, Wilfried A. Kues
Summary: The chicken is one of the most common domestic species worldwide, with a majority originating from hybrid breeding programs. To preserve rare and endangered chicken breeds' genomic resources, innovative methods are necessary. A study conducted on blue layer hybrids successfully established a workflow for deriving and biobanking chicken primordial germ cells (PGCs), demonstrating the potential use of PGCs for the cryobanking of rare breeds or rare alleles.
SCIENTIFIC REPORTS
(2021)
Article
Agriculture, Dairy & Animal Science
Tanja Nolte, Simon Jansen, Steffen Weigend, Daniel Moerlein, Ingrid Halle, Henner Simianer, Ahmad Reza Sharifi
Summary: The study found that the quality of chicken eggs is influenced by genotype and diet composition. Feeding faba beans had an effect on yolk and shell color, Haugh units, and shell portion.
Article
Agriculture, Dairy & Animal Science
Claudia Dierks, Stefanie Altgilbers, Annett Weigend, Rudolf Preisinger, Steffen Weigend
Article
Biotechnology & Applied Microbiology
Johannes Geibel, Nora Paulina Praefke, Steffen Weigend, Henner Simianer, Christian Reimer
Summary: This study aimed to generate a precise SV callset from whole-genome short-read sequencing (WGS) data for three commercial chicken populations and to evaluate the linkage disequilibrium (LD) patterns between the called SVs and surrounding SNPs. The results indicated that LD between deletions (DELs) and SNPs was similar to LD between SNPs, while LD between other SVs and SNPs was significantly reduced. The main reason for the reduced LD was the presence of local minor allele frequency differences. Genotyping accuracy was lower for duplications (DUP), inversions (INV), and translocation breakpoints (BND) compared to SNPs and deletions (DELs). The presence of tag SNPs was slightly lower for DELs compared to WGS SNPs, but this difference disappeared when considering SNPs located on different chicken genotyping arrays.
Article
Physiology
Julia Mehlhorn, Anja Hoehne, Ulrich Baulain, Lars Schrader, Steffen Weigend, Stefanie Petow
Summary: This study analyzed the concentration of estradiol-17β in laying hens of different laying lines at different ages. The results showed that high-performing hens had higher estradiol-17β concentrations compared to low-performing hens. The highest concentration was observed at the 49th to 51st week of age, while the peak of laying intensity was observed at the 33rd to 35th week of age. Additionally, housing conditions influenced the estradiol-17β concentrations, with hens in cages showing higher concentrations compared to those in a floor housing system.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Shijie Lyu, Danny Arends, Mostafa K. Nassar, Annett Weigend, Steffen Weigend, Eryao Wang, Gudrun A. Brockmann
Summary: This study identified genomic regions associated with body size differences between Asian Game and Asian Bantam type chickens through a genome-wide association study and principal component analysis. The investigated Asian Game type chicken breeds were found to be genetically different from the Asian Bantam breeds. A region on chromosome 4 (17.3-21.3 Mb) was identified as potentially contributing to the phenotypic difference, although further validation of candidate genes is necessary.
Article
Multidisciplinary Sciences
Stefanie Altgilbers, Claudia Dierks, Sabine Klein, Steffen Weigend, Wilfried A. Kues
Summary: This study establishes a CRISPR/Cas9-mediated genome editing protocol for modifying primordial germ cells (PGCs) derived from chickens with blue eggshell color. The efficiency of the CRISPR/Cas9 system in introducing large gene deletions in chicken PGCs is demonstrated. The presented workflow provides a cost-effective and rapid solution for screening the editing success in transfected PGCs.
SCIENTIFIC REPORTS
(2022)
Review
Agriculture, Dairy & Animal Science
Hafedh Ben Zaabza, Curtis P. Van Tassell, Jeremie Vandenplas, Paul VanRaden, Zengting Liu, Herwin Eding, Stephanie McKay, Katrine Haugaard, Martin H. Lidauer, Esa A. Mantysaari, Ismo Stranden
Summary: This paper provides an overview of different methods and computational approaches for calculating reliability, from the animal model era to the single-step genomic model era. It also discusses the challenges faced in reliability computation and presents efficient and accurate algorithms developed recently for large-scale genomic evaluations.
JOURNAL OF DAIRY SCIENCE
(2023)
Editorial Material
Genetics & Heredity
Michael N. N. Romanov, Johann Soelkner, Natalia A. A. Zinovieva, Klaus Wimmers, Steffen Weigend
FRONTIERS IN GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
Dorcus Kholofelo Malomane, Steffen Weigend, Armin Otto Schmitt, Annett Weigend, Christian Reimer, Henner Simianer
Summary: Migration of a population from its founder population is expected to reduce genetic diversity and facilitate differentiation between populations, consistent with the theory of genetic isolation by distance. The genetic diversity of domesticated chicken populations is strongly correlated with their genetic distance to wild populations, and this relationship can predict the genetic diversity of domesticated populations. Genes with little genetic variation across populations, such as those associated with brain development, may be more conserved, while genes associated with processes like protein transport and metabolic processes may exhibit faster genetic diversity changes. Overall, these findings contribute to understanding the evolutionary patterns of different functional genomic regions in chicken.
GENETICS SELECTION EVOLUTION
(2021)