scholarly journals Detection of a 4 bp Mutation in the 3′UTR Region of Goat Sox9 Gene and Its Effect on the Growth Traits

Animals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 672 ◽  
Author(s):  
Libang He ◽  
Yi Bi ◽  
Ruolan Wang ◽  
Chuanying Pan ◽  
Hong Chen ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Information Content ◽  
Body Length ◽  
Marker Assisted Selection ◽  
Growth Traits ◽  
Polymorphic Information Content ◽  
Phenotypic Traits ◽  
Breeding Programs ◽  
Cashmere Goats ◽  
Sox9 Gene

The SRY-type HMG box 9 (Sox9) gene plays an important role in chondrocyte development as well as changes in hypertrophic chondrocytes, indicating that Sox9 can regulate growth in animals. However, no studies to date have examined the correlation between variations in Sox9 and growth traits in goats. Here, we found a 4 bp indel in the 3′UTR of Sox9 and verified its association with growth traits in Shaanbei white cashmere goats (n = 1109). The frequencies of two genotypes (ID and II) were 0.397 and 0.603, respectively, and polymorphic information content (PIC) values showed that the indel had a medium PIC (PIC > 0.25). The 4 bp indel was significantly correlated with body length (p = 0.006), heart girth (p = 0.001), and hip width (p = 4.37 × 10 −4). Notably, individuals with the ID genotype had significantly superior phenotypic traits compared with individuals bearing the II genotype. Hence, we speculated that the 4 bp indel is an important mutation affecting growth traits in goat, and may serve as an effective DNA molecular marker for marker-assisted selection in goat breeding programs.

scholarly journals ANALISIS AWAL KERAGAMAN MOLEKULAR KELAPA SAWIT (Elaies guineensis Jacq.) MENGGUNAKAN LIMA PRIMER SSR (Simple Sequences Repeats)

2017 ◽  
Vol 4 (1) ◽  
pp. 47-56
Author(s):  
Arnen Pasaribu
Keyword(s):  
Information Content ◽  
Palm Oil ◽  
Polymorphic Information Content ◽  
Breeding Programs ◽  
Molecular Variance

Molecular variance is very important. The information resulted from the analysis at the molecularlevel can advantage as a first step to manage breeding programs. The aim of thisresearch was to determine a molecular variance in palm oil-based on SSR primer usingFR0465, FR391, FR304, FR0350 and FR3693 primers. The research was conducted atTerpadu Laboratory, Faculty of Medicines, North Sumatera University from September 2015to February 2016. Gen Alex ver. 6.501, Power Marker 3.25 and software DARwin SoftwareVersion 6 was used to calculate and analysis. The result of this research showed that the value ofmolecular variants of Palm Oil (E. guineensis) was 62.43%, polymorphic information content(PIC) was 0.338. The measure of fragment about 120 bp – 496 bp. FR02350 has the highest numberof alel and the value of expected heterozygote (He) was 0.685.

scholarly journals Assessment of genetic diversity of selected cowpea landraces from Nigeria based on simple sequence repeat markers

2020 ◽  
Vol 36 (2) ◽  
pp. 33-44
Author(s):  
I.O. Iseghohi ◽  
A.I. Adesoye ◽  
D.A. Oludare ◽  
F.V. Agunbiade ◽  
N. Unachukwu
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Mantel Test ◽  
Ex Situ ◽  
Breeding Programs ◽  
Ecological Zones ◽  
Landrace Diversity ◽  
Savannah Zone ◽  
Simple Sequence

Understanding the genetic diversity of cowpea (Vigna unguiculata L. Walp.) landraces is useful for effective characterization and ex-situ conservation of germplasm. The analysis of genetic diversity of eighteen cowpea landraces collected from five agro-ecological zones in Nigeria was reported in this study. Five individuals per landrace were genotyped with six polymorphic microsatellite markers. Three to 5 alleles with a mean of 3.833 were detected. Mean Polymorphic information content (PIC) and observed heterozygosity of the markers were 0.5721 and 0.2433, respectively. Analysis of Molecular Variance (AMOVA) showed that variation due to agroecological zone constituted 24%, while variations among and within landraces as well as within individuals constituted 25%, 17% and 33%, respectively. Landraces collected from the humid rainforest zone showed high within landrace diversity and were not significantly different (P ≥ 0.001) from other landraces collected from the same zone. Landraces from the savannah zones showed low within landrace diversity and homozygous across all loci. Consequently, among landrace diversity was higher in the savannah zone with landraces collected from guinea savannah been the most diverse, followed by landraces from the derived savannah and Sudan savannah. Mantel test showed positive and significant correlation (r= 0.377, p= 0.01) between genetic and geographical distance of landrace collections. The findings are important for up-to-date characterizations of cowpea germplasm in Nigeria for improved breeding programs. Keywords: Genetic diversity, cowpea, Alleles, Polymorphic information content, AMOVA,

scholarly journals Genetic and phenotypic diversity of selected Kenyan mung bean (Vigna radiata L. Wilckzek) genotypes

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Jedidah Wangari Mwangi ◽  
Oduor Richard Okoth ◽  
Muchemi Peterson Kariuki ◽  
Ngugi Mathew Piero
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phylogenetic Tree ◽  
Mung Bean ◽  
Phenotypic Diversity ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Phenotypic Traits ◽  
Breeding Programs ◽  
Population Structure Analysis

Abstract Background Mung bean is a pulse crop principally grown in the tropic and subtropic parts of the world for its nutrient-rich seeds. Seven mung beans accessions from Eastern Kenya were evaluated using thirteen phenotypic traits. In addition, 10 SSR markers were used to determine their genetic diversity and population structure. This aimed at enhancing germplasm utilization for subsequent mung bean breeding programs. Results Analysis of variance for most of the phenology traits showed significant variation, with the yield traits recording the highest. The first three principal components (PC) explained 83.4% of the overall phenotypic variation, with the highest (PC1) being due to variation of majority of the traits studied such as pod length, plant height, and seeds per pod. The dendogram revealed that the improved genotypes had common ancestry with the local landraces. The seven mung beans were also genotyped using 10 microsatellite markers, eight of which showed clear and consistent amplification profiles with scorable polymorphisms in all the studied genotypes. Genetic diversity, allele number, and polymorphic information content (PIC) were determined using powermarker (version 3.25) and phylogenetic tree constructed using DARWIN version 6.0.12. Analysis of molecular variance (AMOVA) was calculated using GenALEx version 6.5. A total of 23 alleles were detected from the seven genotypes on all the chromosomes studied with an average of 2.875 across the loci. The PIC values ranged from 0.1224 (CEDG056) to 0.5918 (CEDG092) with a mean of 0.3724. Among the markers, CEDG092 was highly informative while the rest were reasonably informative except CEDG056, which was less informative. Gene diversity ranged from 0.1836 (CEDG050) to 0.5102 (CDED088) with an average of 0.3534. The Jaccards dissimilarity matrix indicated that genotypes VC614850 and N26 had the highest level of dissimilarity while VC637245 and N26 had lowest dissimilarity index. The phylogenetic tree grouped the genotypes into three clusters as revealed by population structure analysis (K = 3), with cluster III having one unique genotype (VC6137B) only. AMOVA indicated that the highest variation (99%) was between individual genotype. In addition, marker traits association analysis revealed 18 significant associations (P < 0.05). Conclusion These findings indicate sufficient variation among the studied genotypes that can be considered for germplasm breeding programs.

scholarly journals Plant breeding with marker-assisted selection in Brazil

2014 ◽  
Vol 14 (1) ◽  
pp. 54-60 ◽  
Author(s):  
Ney Sussumu Sakiyama ◽  
Helaine Christine Cancela Ramos ◽  
Eveline Teixeira Caixeta ◽  
Messias Gonzaga Pereira
Keyword(s):  
Molecular Marker ◽  
Plant Breeding ◽  
Marker Assisted Selection ◽  
Public Institutions ◽  
Breeding Program ◽  
Breeding Programs ◽  
Know How ◽  
The Past ◽  
Seed Market ◽  
Marker Studies

Over the past three decades, molecular marker studies reached extraordinary advances, especially for sequencing and bioinformatics techniques. Marker-assisted selection became part of the breeding program routines of important seed companies, in order to accelerate and optimize the cultivar developing processes. Private seed companies increasingly use marker-assisted selection, especially for the species of great importance to the seed market, e.g. corn, soybean, cotton, and sunflower. In the Brazilian public institutions few breeding programs use it efficiently. The possible reasons are: lack of know-how, lack of appropriate laboratories, few validated markers, high cost, and lack of urgency in obtaining cultivars. In this article we analyze the use and the constraints of marker-assisted selection in plant breeding programs of Brazilian public institutes.

scholarly journals Biometric Characterization of the Portuguese Autochthonous Hens Breeds

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 498
Author(s):  
Nuno V. Brito ◽  
Júlio C. Lopes ◽  
Virgínia Ribeiro ◽  
Rui Dantas ◽  
José V. Leite
Keyword(s):  
Sexual Dimorphism ◽  
Body Length ◽  
Principal Component ◽  
Modern Society ◽  
Phenotypic Traits ◽  
Breeding Programs ◽  
Dual Purpose ◽  
Cultural Legacy ◽  
Marginal Areas

Promotion of the conservation and preservation of local breed’s biodiversity combined with the concept of sustainable agriculture and development of economically marginal areas are important policies to implement in modern society. The biometric characterization, contributing to maintain phenotypic traits, is a significant tool in breeding programs, which revaluate local breeds, allow the preservation of animal biodiversity and support consumer demands. This paper approaches the biometric characterization of the Portuguese poultry breeds through the study of sexual dimorphism and breed differentiation using six zoometric measures as differentiation criteria. A total of 429 fowl (66 males and 426 females) were studied and the parameters recorded were body weight, body length, chest circumference, shank length, shank diameter and wingspan. A highly sexual dimorphism was evident, in all breeds, with the “Branca” breed being the most zoometrically distant. Concerning Principal Component Analysis, the highly correlations observed between body length, wingspan and shank length, determined the generalized animal form and could be used as selection criteria for improving body size. Breeding programs aiming to preserve these local genetic resources should consider the dual purpose of these breeds: sustainability and cultural legacy, and the offer to urban consumers a source of differentiated high-quality products.

Improving the Resistance of Wuyunjing 8 to Rice Stripe Virus via Molecular Marker-assisted Selection

2011 ◽  
Vol 37 (5) ◽  
pp. 745-754 ◽  
Author(s):  
Hong-Gen ZHANG ◽  
Zuo-Peng XU ◽  
Peng LI ◽  
Bo LI ◽  
Chao LIU ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Marker Assisted Selection ◽  
Rice Stripe Virus

scholarly journals A Novel 13 bp Deletion within the NR6A1 Gene Is Significantly Associated with Growth Traits in Donkeys

Animals ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 681 ◽  
Author(s):  
Xiya Fang ◽  
Zhenyu Lai ◽  
Jie Liu ◽  
Chunlan Zhang ◽  
Shipeng Li ◽  
...  
Keyword(s):  
Nuclear Receptor ◽  
Growth Traits ◽  
Polyacrylamide Gel Electrophoresis ◽  
Embryonic Stem ◽  
The Body ◽  
Economic Traits ◽  
Breeding Programs ◽  
Intron 1 ◽  
Group A ◽  
Nuclear Receptor Family

Nuclear receptor subfamily 6, group A, member 1 (NR6A1), as an important member of the nuclear receptor family, plays an important role in regulating growth, metabolism, and differentiation of embryonic stem cells. For this reason, the NR6A1 gene is considered to be a promising candidate for economic traits and was found to be associated with body size traits in many livestock. However, no studies have been conducted on NR6A1 in donkeys so far. Thus, in this research, we focused on donkeys and identified a 13 bp deletion in intron-1 of the NR6A1 gene among 408 individuals from Guanzhong and Dezhou donkeys using polyacrylamide gel electrophoresis. Three genotypes were identified, namely II, ID, and DD. The association analysis indicated that the body lengths and body heights5f genotype II individuals were significantly different to those of genotype ID in Dezhou donkeys. Conclusively, the 13 bp deletion was associated with growth traits in both Guanzhong donkeys and Dezhou donkeys, indicating that the NR6A1 gene could be a possible candidate gene in marker-assisted selection for donkey breeding programs.

scholarly journals Mapping QTL for spike fertility and related traits in two doubled haploid wheat (Triticum aestivum L.) populations

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Nicole Pretini ◽  
Leonardo S. Vanzetti ◽  
Ignacio I. Terrile ◽  
Guillermo Donaire ◽  
Fernanda G. González
Keyword(s):  
Doubled Haploid ◽  
Marker Assisted Selection ◽  
Triticum Aestivum L ◽  
Physiological Model ◽  
Yield Potential ◽  
Breeding Programs ◽  
Per Se ◽  
Genomic Regions ◽  
Fertility Traits ◽  
Selection Of

Abstract Background In breeding programs, the selection of cultivars with the highest yield potential consisted in the selection of the yield per se, which resulted in cultivars with higher grains per spike (GN) and occasionally increased grain weight (GW) (main numerical components of the yield). In this study, quantitative trait loci (QTL) for GW, GN and spike fertility traits related to GN determination were mapped using two doubled haploid (DH) populations (Baguette Premium 11 × BioINTA 2002 and Baguette 19 × BioINTA 2002). Results In total 305 QTL were identified for 14 traits, out of which 12 QTL were identified in more than three environments and explained more than 10% of the phenotypic variation in at least one environment. Eight hotspot regions were detected on chromosomes 1A, 2B, 3A, 5A, 5B, 7A and 7B in which at least two major and stable QTL sheared confidence intervals. QTL on two of these regions (R5A.1 and R5A.2) have previously been described, but the other six regions are novel. Conclusions Based on the pleiotropic analysis within a robust physiological model we conclude that two hotspot genomic regions (R5A.1 and R5A.2) together with the QGW.perg-6B are of high relevance to be used in marker assisted selection in order to improve the spike yield potential. All the QTL identified for the spike related traits are the first step to search for their candidate genes, which will allow their better manipulation in the future.

scholarly journals Genomic Analysis, Progress and Future Perspectives in Dairy Cattle Selection: A Review

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 599
Author(s):  
Miguel A. Gutierrez-Reinoso ◽  
Pedro M. Aponte ◽  
Manuel Garcia-Herreros
Keyword(s):  
Dairy Cattle ◽  
Production Efficiency ◽  
Association Studies ◽  
Phenotypic Traits ◽  
Progeny Testing ◽  
Genome Wide Association Studies ◽  
Genetic Progress ◽  
Breeding Programs ◽  
Increased Risk ◽  
Selection Of

Genomics comprises a set of current and valuable technologies implemented as selection tools in dairy cattle commercial breeding programs. The intensive progeny testing for production and reproductive traits based on genomic breeding values (GEBVs) has been crucial to increasing dairy cattle productivity. The knowledge of key genes and haplotypes, including their regulation mechanisms, as markers for productivity traits, may improve the strategies on the present and future for dairy cattle selection. Genome-wide association studies (GWAS) such as quantitative trait loci (QTL), single nucleotide polymorphisms (SNPs), or single-step genomic best linear unbiased prediction (ssGBLUP) methods have already been included in global dairy programs for the estimation of marker-assisted selection-derived effects. The increase in genetic progress based on genomic predicting accuracy has also contributed to the understanding of genetic effects in dairy cattle offspring. However, the crossing within inbred-lines critically increased homozygosis with accumulated negative effects of inbreeding like a decline in reproductive performance. Thus, inaccurate-biased estimations based on empirical-conventional models of dairy production systems face an increased risk of providing suboptimal results derived from errors in the selection of candidates of high genetic merit-based just on low-heritability phenotypic traits. This extends the generation intervals and increases costs due to the significant reduction of genetic gains. The remarkable progress of genomic prediction increases the accurate selection of superior candidates. The scope of the present review is to summarize and discuss the advances and challenges of genomic tools for dairy cattle selection for optimizing breeding programs and controlling negative inbreeding depression effects on productivity and consequently, achieving economic-effective advances in food production efficiency. Particular attention is given to the potential genomic selection-derived results to facilitate precision management on modern dairy farms, including an overview of novel genome editing methodologies as perspectives toward the future.

scholarly journals Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Workia Ahmed ◽  
Tileye Feyissa ◽  
Kassahun Tesfaye ◽  
Sumaira Farrakh
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Information Content ◽  
Date Palm ◽  
Polymorphic Information Content ◽  
Phoenix Dactylifera ◽  
Mean Value ◽  
Date Palms ◽  
Expected Heterozygosity

Abstract Background Date palm tree (Phoenix dactylifera L.) is a perennial monocotyledonous plant belonging to the Arecaceae family, a special plant with extraordinary nature that gives eminent contributions in agricultural sustainability and huge socio-economic value in many countries of the world including Ethiopia. Evaluation of genetic diversity across date palms at DNA level is very important for breeding and conservation. The result of this study could help to design for genetic improvement and develop germplasm introduction programmes of date palms mainly in Ethiopia. Results In this study, 124 date palm genotypes were collected, and 10 polymorphic microsatellite markers were used. Among 10 microsatellites, MPdCIR085 and MPdCIR093 loci showed the highest value of observed and expected heterozygosity, maximum number of alleles, and highest polymorphic information content values. A total of 112 number of alleles were found, and the mean number of major allele frequency was 0.26, with numbers ranging from 0.155 (MPdCIR085) to 0.374 (MPdCIR016); effective number of alleles with a mean value of 6.61, private alleles ranged from 0.0 to 0.65; observed heterozygosity ranged from 0.355 to 0.726; expected heterozygosity varied from 0.669 to 0.906, polymorphic information content with a mean value of 0.809; fixation index individuals relative to subpopulations ranged from 0.028 for locus MPdCIR032 to 0.548 for locus MPdCIR025, while subpopulations relative to total population value ranged from − 0.007 (MPdCIR070) to 0.891 (MPdCIR015). All nine accesstions, neighbour-joining clustering analysis, based on dissimilarity coefficient values were grouped into five major categories; in population STRUCTURE analysis at highest K value, three groups were formed, whereas DAPC separated date palm genotypes into eight clusters using the first two linear discriminants. Principal coordinate analysis was explained, with a 17.33% total of variation in all populations. Generally, the result of this study revealed the presence of allele variations and high heterozygosity (> 0.7) in date palm genotypes. Conclusions Microsatellites (SSR) are one of the most preferable molecular markers for the study of genetic diversity and population structure of plants. In this study, we found the presence of genetic variations of date palm genotypes in Ethiopia; therefore, these genetic variations of date palms is important for crop improvement and conservation programmes; also, it will be used as sources of information to national and international genbanks.

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