Article
Agricultural Engineering
Raghu Tamang, Sunita Munda, Rose Laldinaii Darnei, Twahira Begum, Mohan Lal
Summary: In this study, molecular diversity analysis was performed on 138 Acorus calamus accessions from Northeast India using SSR markers. The results showed a high level of polymorphism, with 186 polymorphic alleles identified. AMOVA analysis revealed significant genetic variations within and among populations, and three genetically diverse populations were identified through dendrogram analysis and principal component analysis. This is the first report on the molecular diversity of A. calamus using SSR markers, and it has important implications for crop improvement, conservation, and elite genotype identification.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Entomology
Ali Milton, Dennis Muhanguzi, Allan Male, Ali Kajubi, Stephen Buah, Jerome Kubiriba, Robooni Tumuhimbise
Summary: This study aimed to develop a cheap and easily accessible genotyping method for the banana weevil. By using transcriptome-derived SSR markers, the genetic diversity of banana weevil populations in different regions of Uganda was analyzed, providing valuable information for integrated pest management strategies.
JOURNAL OF ECONOMIC ENTOMOLOGY
(2022)
Article
Agronomy
Scott E. E. Warnke, Jinyoung Y. Y. Barnaby
Summary: The study introduces the characteristics and resistance of colonial bentgrass (Agrostis capillaris) to fungal disease and water-deficit stress, as well as the possibility of hybridization with creeping bentgrass (Agrostis stolonifera). Through genetic marker screening, limited genetic diversity was found among nine colonial bentgrass cultivars and one creeping bentgrass cultivar. These genetic markers may be useful for selecting genotypes with enhanced interspecific hybridization potential.
Article
Genetics & Heredity
Yicheng Zhong, Yue Wang, Zhimin Sun, Juan Niu, Yaliang Shi, Kunyong Huang, Jing Chen, Jianhua Chen, Mingbao Luan
Summary: Genetic diversity and structure of 955 Akebia trifoliata germplasms were assessed using 28 SSR markers, revealing moderate polymorphism and weak genetic structure. Specific characters could completely distinguish the germplasms, and a core collection of 164 germplasms was identified with significantly different diversity parameters compared to a random core collection. These findings have implications for germplasm conservation and utilization.
FRONTIERS IN GENETICS
(2021)
Article
Horticulture
Lei Zhu, Huayu Zhu, Yanman Li, Yong Wang, Xiangbin Wu, Jintao Li, Zhenli Zhang, Yanjiao Wang, Jianbin Hu, Sen Yang, Luming Yang, Shouru Sun
Summary: Simple sequence repeats (SSRs) were widely identified in Cucurbita species, with dinucleotide motifs being the most common type. The majority of SSR loci were suitable for marker development and played a crucial role in genetic analysis.
Article
Plant Sciences
Moldir Yermagambetova, Shyryn Almerekova, Orzimat Turginov, Ormon Sultangaziev, Saule Abugalieva, Yerlan Turuspekov
Summary: The genetic diversity and population structure of 15 populations of Juniperus seravschanica from Central Asia were studied using 11 SSR markers. The results showed high genetic diversity and a relatively dispersed population structure, providing valuable data for future conservation strategies.
Article
Plant Sciences
Yi Lu, Jianling Chen, Bing Chen, Qianqian Liu, Hanlin Zhang, Liyuan Yang, Zhi Chao, Enwei Tian
Summary: This study provides a comprehensive investigation into the genetic diversity and population structure of F.hirta in southern China. The results reveal high genetic diversity and low population differentiation in this medicinal plant. The causes of the current genetic patterns are clarified, and insights are provided for the exploitation and conservation strategies of F.hirta.
Article
Forestry
Zeliang Wang, Yi Lin, Xiongcai Gou, Jincheng Du, Maolin Wang
Summary: In this study, genetic variation in ten populations of C. yunnanensis in Sichuan Province was assessed using nine SSR markers. The results revealed high genetic diversity in C. yunnanensis, with the population divided into three clusters. This study provides valuable information for genetic improvement efforts.
Article
Plant Sciences
Chenxing Zhang, Chunfeng Jia, Xinru Liu, Hanqing Zhao, Lu Hou, Meng Li, Binbin Cui, Yingyue Li
Summary: This study assessed the transferability of SSR markers from other species of Lamiaceae to Elsholtzia stauntonii and identified 10 highly polymorphic markers for analyzing genetic variation in natural populations in Hebei Province, China. The results showed low gene flow and high genetic differentiation among populations. By using STRUCTURE analysis, UPGMA clustering, and principal coordinate analysis, the samples were grouped into two clusters based on geographical provenance, consistent with the results of a Mantel test.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Antonio Calvi, Meriem Miyassa Aci, Antonio Lupini, Giovanni Preiti
Summary: This study investigated the morphological traits and genetic diversity of wild hops in the Calabria region of South Italy. Cone length showed significant variation among different populations, while cone shape was the most discriminant trait. Genetic diversity analysis using eight SSR markers revealed high genetic variability in Calabria, and genetic structure analysis identified two distinct groups regardless of the sampling sites. Further research will be conducted to explore other wild hops populations in Calabria and identify specific alleles for new breeding programs.
Article
Agronomy
Li Cheng, Bing Cao, Shuangling Xie, Luyang Yang, Yunyu Zhang, Qinhua Cheng, Juan Liu, Suqin Yu, Dongnan Hu
Summary: This study analyzed the genetic diversity of 11 wild Camellia oleifera populations in Xinxian County, the northern margin of the distribution of C. oleifera in China. The results showed that these populations had high genetic diversity, with low genetic differentiation between populations. The genetic variation mainly came from within the population. This study provides a theoretical and scientific basis for the future development and utilization of wild C. oleifera resources and breeding.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Agronomy
Manosh Kumar Biswas, Dhiman Biswas, Mita Bagchi, Ganjun Yi, Guiming Deng
Summary: Microsatellites, or SSRs, were identified in pre-miRNA sequences from 292 plant species in six taxonomic groups, with 51% of sequences containing SSRs, mainly mononucleotide, di- and trinucleotide repeats. There were 9,498 potential microsatellite loci as pre-miRNA SSR markers, with about 65.51% of primer pairs transferable to at least one plant taxonomic group. The data presented accelerate understanding of pre-miRNA evolution and serve as valuable genomic resources for genetic improvements in a variety of crops.
Article
Agriculture, Multidisciplinary
Wei-Hong Sun, Fei-Fei Wu, Lili Cong, Mei-Yan Jin, Xian-Guo Wang
Summary: The genetic diversity of the Vicia genus was analyzed using SSR markers. The results indicated that the markers were highly informative, clarifying the genetic diversity and population structure of Vicia.
Article
Forestry
Dongye Lu, Haiguang Huang, Aijun Wang, Guosheng Zhang
Summary: In this study, the genetic diversity and genetic structure of 11 populations of Juniperus sabina in northwest China were evaluated using SSRs, and isolation barriers were predicted. The results showed that geographic isolation is the main factor affecting the genetic structure of J. sabina populations. These findings provide a foundation for the genetic conservation and management of J. sabina.
Article
Agronomy
Sundas Shahzad, Muhammad Saeed, Shagufta Perveen, Muhammad Azeem, Iqra Sajjad, Shazia Saeed, Muhammad Naeem, Alia Javed, Iqra Sultan, Ukasha Faria, Sana Maryam, Muhammad Zaid Yousaf
Summary: In this study, genetic diversity and population structure of sixty Saccharum spp. hybrids were assessed using SSR markers. The results showed that SSR markers were effective tools for evaluating genetic diversity and varietal fingerprinting in sugarcane hybrids, which could aid in selecting the best parents for planned crosses.
GENETIC RESOURCES AND CROP EVOLUTION
(2022)
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
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
Christin Habig, Martina Henning, Ulrich Baulain, Simon Jansen, Armin Manfred Scholz, Steffen Weigend
Summary: The study conducted experiments on laying hens in different environments and species conditions, observed the keel bone damage situation, and identified some related factors, to some extent explaining the reasons for keel bone damage in laying hens.
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)