scholarly journals Genetic Variability in Local and Imported Germplasm Chicken Populations as Revealed by Analyzing Runs of Homozygosity

Animals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1887
Author(s):  
Natalia V. Dementieva ◽  
Andrei A. Kudinov ◽  
Tatiana A. Larkina ◽  
Olga V. Mitrofanova ◽  
Artyom P. Dysin ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Germplasm Collection ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Breeding Programs ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Rare And Endangered ◽  
Chicken Breeds ◽  
Conservation Breeding

Preserving breed uniqueness and purity is vitally important in developing conservation/breeding programs for a germplasm collection of rare and endangered chicken breeds. The present study was aimed at analyzing SNP genetic variability of 21 small local and imported purebred and F1 crossbred populations and identifying crossbreeding events via whole-genome evaluation of runs of homozygosity (ROH). The admixture models more efficiently reflected population structure, pinpointing crossbreeding events in the presence of ancestral populations but not in their absence. Multidimensional scaling and FST-based analyses did not discriminate properly between purebred populations and F1 crossbreds, especially when comparing related breeds. When applying the ROH-based approach, more and longer ROHs were revealed in purebred individuals/populations, suggesting this as an effective implement in genome-wide analysis of germplasm breed purity.

scholarly journals Genetic variability and genome-wide association analysis of flavor and texture in cooked beans (Phaseolus vulgaris L.)

2021 ◽  
Author(s):  
Amber Bassett ◽  
Kelvin Kamfwa ◽  
Daniel Ambachew ◽  
Karen Cichy
Keyword(s):  
Genetic Variability ◽  
Seed Coat ◽  
Principal Component ◽  
Breeding Programs ◽  
Flavor Intensity ◽  
Genome Wide ◽  
White Bean ◽  
The Usa ◽  
New Varieties ◽  
End Use

Abstract Key message Cooked bean flavor and texture vary within and across 20 Andean seed types; SNPs are significantly associated with total flavor, beany, earthy, starchy, bitter, seed-coat perception, and cotyledon texture. Abstract Common dry beans are a nutritious food recognized as a staple globally, but their consumption is low in the USA. Improving bean flavor and texture through breeding has the potential to improve consumer acceptance and suitability for new end-use products. Little is known about genetic variability and inheritance of bean sensory characteristics. A total of 430 genotypes of the Andean Diversity Panel representing twenty seed types were grown in three locations, and cooked seeds were evaluated by a trained sensory panel for flavor and texture attribute intensities, including total flavor, beany, vegetative, earthy, starchy, sweet, bitter, seed-coat perception, and cotyledon texture. Extensive variation in sensory attributes was found across and within seed types. A set of genotypes was identified that exhibit extreme attribute intensities generally stable across all three environments. seed-coat perception and total flavor intensity had the highest broad-sense heritability (0.39 and 0.38, respectively), while earthy and vegetative intensities exhibited the lowest (0.14 and 0.15, respectively). Starchy and sweet flavors were positively correlated and highest in white bean genotypes according to principal component analysis. SNPs associated with total flavor intensity (six SNPs across three chromosomes), beany (five SNPs across four chromosomes), earthy (three SNPs across two chromosomes), starchy (one SNP), bitter (one SNP), seed-coat perception (three SNPs across two chromosomes), and cotyledon texture (two SNPs across two chromosomes) were detected. These findings lay a foundation for incorporating flavor and texture in breeding programs for the development of new varieties that entice growers, consumers, and product developers alike.

scholarly journals Genetic analysis of sucrose concentration in soybean seeds using a historical soybean genomic panel

2021 ◽  
Author(s):  
Alexandra Ficht ◽  
Robert W. Bruce ◽  
Davoud Torkamaneh ◽  
Christopher Grainger ◽  
Milad Eskandari ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Genome Wide Association Study ◽  
Sucrose Concentration ◽  
Soybean Seed ◽  
Breeding Programs ◽  
Snp Data ◽  
Genome Wide ◽  
A Genome ◽  
Important Trait ◽  
Genotype By Sequencing

Abstract Soybean (Glycine max (L.) Merr) is a crop of global importance for both human and animal consumption, which was domesticated in China more than 6000 years ago. A concern about losing genetic diversity as a result of decades of breeding has been expressed by soybean researchers. In order to develop new cultivars, it is critical for breeders to understand the genetic variability present for traits of interest in their program germplasm. Sucrose concentration is becoming an increasingly important trait for the production of soy-food products. The objective of this study was to use a genome-wide association study (GWAS) to identify putative QTL for sucrose concentration in soybean seed. A GWAS panel consisting of 266 historic and current soybean accessions was genotyped with 76k genotype-by-sequencing (GBS) SNP data and phenotyped in four field locations in Ontario (Canada) from 2015 to 2017. Seven putative QTL were identified on chromosomes 1, 6, 8, 9, 10, 13 and 14. A key gene related to sucrose synthase (Glyma.06g182700) was found to be associated with the QTL found on chromosome 6. This information will facilitate efforts to increase the available genetic variability for sucrose concentration in soybean breeding programs and develop new and improved high-sucrose soybean cultivars suitable for the soy-food industry.

Genome-wide analysis of the expansin gene superfamily reveals Brassica rapa-specific evolutionary dynamics upon whole genome triplication

2014 ◽  
Vol 290 (2) ◽  
pp. 521-530 ◽  
Author(s):  
Panneerselvam Krishnamurthy ◽  
Joon Ki Hong ◽  
Jin A Kim ◽  
Mi-Jeong Jeong ◽  
Yeon-Hee Lee ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Evolutionary Dynamics ◽  
Whole Genome ◽  
Genome Wide Analysis ◽  
Expansin Gene ◽  
Genome Wide ◽  
Genome Triplication

scholarly journals Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Hequan Sun ◽  
Beth A. Rowan ◽  
Pádraic J. Flood ◽  
Ronny Brandt ◽  
Janina Fuss ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Chromosome Segregation ◽  
Meiotic Recombination ◽  
Whole Genome ◽  
Fine Scale ◽  
Simultaneous Generation ◽  
Genome Wide Analysis ◽  
Recombinant Plant ◽  
Genome Wide ◽  
Large Populations

Abstract Meiotic crossovers (COs) ensure proper chromosome segregation and redistribute the genetic variation that is transmitted to the next generation. Large populations and the demand for genome-wide, fine-scale resolution challenge existing methods for CO identification. Taking advantage of linked-read sequencing, we develop a highly efficient method for genome-wide identification of COs at kilobase resolution in pooled recombinants. We first test this method using a pool of Arabidopsis F2 recombinants, and recapitulate results obtained from the same plants using individual whole-genome sequencing. By applying this method to a pool of pollen DNA from an F1 plant, we establish a highly accurate CO landscape without generating or sequencing a single recombinant plant. The simplicity of this approach enables the simultaneous generation and analysis of multiple CO landscapes, accelerating the pace at which mechanisms for the regulation of recombination can be elucidated through efficient comparisons of genotypic and environmental effects on recombination.

scholarly journals Induction of theCandida albicansFilamentous Growth Program by Relief of Transcriptional Repression: A Genome-wide Analysis

2005 ◽  
Vol 16 (6) ◽  
pp. 2903-2912 ◽  
Author(s):  
David Kadosh ◽  
Alexander D. Johnson
Keyword(s):  
Candida Albicans ◽  
Transcriptional Repression ◽  
Fungal Pathogen ◽  
Morphological Transition ◽  
Whole Genome ◽  
Transcriptional Repressors ◽  
Genome Wide Analysis ◽  
Human Fungal Pathogen ◽  
Genome Wide ◽  
A Genome

Candida albicans, the major human fungal pathogen, undergoes a reversible morphological transition from blastospores (round budding cells) to filaments (elongated cells attached end-to-end). This transition, which is induced upon exposure of C. albicans cells to a number of host conditions, including serum and body temperature (37°C), is required for virulence. Using whole-genome DNA microarray analysis, we describe 61 genes that are significantly induced (≥2-fold) during the blastospore to filament transition that takes place in response to exposure to serum and 37°C. We next show that approximately half of these genes are transcriptionally repressed in the blastospore state by three transcriptional repressors, Rfg1, Nrg1, and Tup1. We conclude that the relief of this transcriptional repression plays a key role in bringing the C. albicans filamentous growth program into play, and we describe the framework of this transcriptional circuit.

scholarly journals Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 524 ◽  
Author(s):  
Sangang He ◽  
Jiang Di ◽  
Bing Han ◽  
Lei Chen ◽  
Mingjun Liu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Average Length ◽  
Inbreeding Coefficient ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Genotyping Array ◽  
Genome Region ◽  
Genome Wide ◽  
Genomic Regions ◽  
Genome Wide Scan

In this study, we estimated the number, length, and frequency of runs of homozygosity (ROH) in 635 Chinese Merino and identified genomic regions with high ROH frequency using the OvineSNP50 whole-genome genotyping array. A total of 6039 ROH exceeding 1 Mb were detected in 634 animals. The average number of ROH in each animal was 9.23 and the average length was 5.87 Mb. Most of the ROH were less than 10 Mb, accounting for 88.77% of the total number of detected ROH. In addition, Ovies aries chromosome (OAR) 21 and OAR3 exhibited the highest and lowest coverage of chromosomes by ROH, respectively. OAR1 displayed the highest number of ROH, while the lowest number of ROH was found on OAR24. An inbreeding coefficient of 0.023 was calculated from ROH greater than 1 Mb. Thirteen regions on chromosomes 1, 2, 3, 5, 6, 10, 11, and 16 were found to contain ROH hotspots. Within the genome regions of OAR6 and OAR11, NCAPG/LCORL, FGF11 and TP53 were identified as the candidate genes related to body size, while the genome region of OAR10 harbored RXFP2 gene responsible for the horn trait. These findings indicate the adaptive to directional trait selection in Chinese Merino.

scholarly journals Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Laura Iacolina ◽  
Astrid V. Stronen ◽  
Cino Pertoldi ◽  
Małgorzata Tokarska ◽  
Louise S. Nørgaard ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Cattle Breed ◽  
European Bison ◽  
Nucleotide Polymorphisms ◽  
Runs Of Homozygosity ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Visual Identification ◽  
Genome Wide ◽  
Or Groups

Runs of homozygosity (ROH), uninterrupted stretches of homozygous genotypes resulting from parents transmitting identical haplotypes to their offspring, have emerged as informative genome-wide estimates of autozygosity (inbreeding). We used genomic profiles based on 698 K single nucleotide polymorphisms (SNPs) from nine breeds of domestic cattle (Bos taurus) and the European bison (Bison bonasus) to investigate how ROH distributions can be compared within and among species. We focused on two length classes: 0.5–15 Mb to investigate ancient events and >15 Mb to address recent events (approximately three generations). For each length class, we chose a few chromosomes with a high number of ROH, calculated the percentage of times a SNP appeared in a ROH, and plotted the results. We selected areas with distinct patterns including regions where (1) all groups revealed an increase or decrease of ROH, (2) bison differed from cattle, (3) one cattle breed or groups of breeds differed (e.g., dairy versus meat cattle). Examination of these regions in the cattle genome showed genes potentially important for natural and human-induced selection, concerning, for example, meat and milk quality, metabolism, growth, and immune function. The comparative methodology presented here permits visual identification of regions of interest for selection, breeding programs, and conservation.

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