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The Kermani sheep has adapted to a tropical region and is an important meat producing animal in Iran and its economic efficiency is mainly dependent on its growth and reproduction ability. The ability of a population to respond adaptively to environmental changes depends on its level of genetic variability or diversity. Thus, genetic diversity in i...
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In the agricultural sector, it is important to identify the main directions of investment in order to ensure the food supply for the country's population. One of the most important cases in this sector is ensuring the secure supply of meat and meat products. The state has to choose the most effective tools for supporting the development of indigeno...
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... In sheep, the (AG)9C ISSR marker has a significant effect on body weight (Zamani et al., 2015;Mohammadabadi, 2016). Thus, this marker has an I value of 0.25 for Mehraban sheep (Zamani et al., 2011) and 1.03 for Kermani sheep (Mohammadabadi et al., 2017). Moreover, the (AG)9C ISSR marker of Tuvinian short-fat-tailed sheep reveals the ne, I, and PIC values of about 1.24; 0.22, and 0.45, respectively (Stolpovsky et al., 2010). ...
Background. Bali cattle (Bos javanicus) are Indonesian native cattle that are kept as beef cattle. Among Bali cattle, however, there are white Bali cattle, called Taro cattle which are found in small numbers of the population and used only for religious ceremony needs. Objective. To quantify the genetic variation in two phenotypes of Bali cattle (wildtype and white colors) with inter-simple sequence repeat (ISSR) primer of (AG)9C. Methodology. Forty Bali cattle, 20 wildtype bulls, and 20 white Bali cows were used. The blood samples were taken from the jugular vein of each animal using venoject vacutainer tube containing EDTA. The DNA extraction was performed using DNA extraction kit following the manufacturer's protocol. Number of DNA fragments, number of effective alleles (ne), and polymorphic informative content (PIC) were calculated to describe the genetic diversity in animals under study. Results: Results showed that three haplotype (H) types were observed in the animals under this study based on the ISSR fragments. The polymorphic informative content (PIC) in the white animals was higher than in the wild-type animals (0.62 vs 0.18). According to (AG)9C ISSR marker, mostly white (50%) and wildtype (90%) animals were classified into H2 type. Therefore, a total of 25% of white and 10% of wild-type animals were classified into H3 type. While 25% of white animals were classified into H1 type. Implications. the information generated in this study can be used as early information to investigate the molecular genetics of Taro cattle. Conclusions: This study suggests that many white animals have a specific locus which is absent in wild-type animals.
... The effective number of alleles (Ne) in our case was found to be 1.013 ± 0.00034. In this case, low-frequency alleles have little contribution to the effective number of alleles (Mohammadabadi et al. 2017). It is a very informative parameter for establishing collection strategies while creating a representative sub-population for a larger data set. ...
Unlabelled:
To unravel the plastid genome diversity among the cultivated groups of the pigeonpea germplasm, we characterized the SNP occurrence and distribution of 142 pigeonpea mini-core collections based on their reference-based assembly of the chloroplast genome. A total of 8921 SNPs were found, which were again filtered and finally 3871 non-synonymous SNPs were detected and used for diversity estimates. These 3871 SNPs were classified into 12 groups and were present in only 44 of the 125 genes, demonstrating the presence of a precise mechanism for maintaining the whole chloroplast genome throughout evolution. The Acetyl-CoA carboxylase D gene possesses the maximum number of SNPs (12.29%), but the Adenosine Tri-Phosphate synthatase cluster genes (atpA, atpB, atpE, atpF, atpH, and atpI) altogether bear 43.34% of the SNPs making them most diverse. Various diversity estimates, such as the number of effective alleles (1.013), Watterson's estimate (0.19), Tajima's D ( - 3.15), Shannon's information index (0.036), suggest the presence of less diversity in the cultivated gene pool of chloroplast genomes. The genetic relatedness estimates based on pairwise correlations were also in congruence with these diversity descriptors and indicate the prevalence of rare alleles in the accessions. Interestingly, no stratification was observed either through STRUCTURE, PCoA, or phylogenetic analysis, indicating the common origin of the chloroplast in all the accessions used, irrespective of their geographical distribution. Further 6194 Cleaved Amplified Polymorphic Sequences (CAPS) markers for 531 SNPs were developed and validated in a selected set of germplasm. Based on these results, we inferred that all of the cultivated gene pools of pigeonpea have a common origin for the chloroplast genome and they possess less diversity in protein-coding regions, indicating a stable and evolved plastid genome. At the same time, all diversity analysis indicates the occurrence of rare alleles, suggesting the suitability of the mini-core collection in future pigeonpea improvement programs. In addition, the development of chloroplast genome-based CAPS markers would have utility in pigeonpea breeding programs.
Supplementary information:
The online version contains supplementary material available at 10.1007/s13205-023-03785-8.
... نشانگرهای شناسایی برای ارتباطی تجزیه از استفاده Askari et al., 2010;Ghasemi et al., 2010;Askari et al., 2011;Zamani et al., 2011;Mohammadabadi and Askari 2012;Zamani et al., 2015;Bahador et al., 2016;Mohammadabadi et al., 2017;Mohammadabadi et al. 2021 . مختلط ( Mixed ) G21 Isf-1 0.42 0.58 مختلط ( Mixed ) G02 Raf1_2 0.24 0.76 سبز ( Green ) G22 Isf-2 0.46 0.54 مختلط ( Mixed ) G03 Raf1_3 0.41 0.59 مختلط ( Mixed ) G23 Isf-3 0.43 0.57 مختلط ( Mixed ) G04 Raf1_4 0.15 0.85 سبز ( Green ) G24 Isf-4 0.37 0.63 مختل ط ( Mixed ) G05 Ard-1 0.32 0.68 مختلط ( Mixed ) G25 Ham1_ 1 0.46 0.54 مختلط ( Mixed ) G06 Ard-2 0.13 0.87 سبز ( Green ) G26 Ham1_ 2 0.39 0.61 مختلط ( Mixed ) G07 Ard-3 0.47 0.53 مختلط ( Mixed ) G27 Ham1_ 3 0.48 0.52 مختلط ( Mixed ) G08 Ard-4 0.36 0.64 مختلط ( Mixed ) G28 Ham1_ 4 0.62 0.38 مختلط ( Mixed ) G09 Raf2_1 0.15 0.85 سبز ( Green ) G29 Ham2_ 1 0.78 0.23 قرمز ( Red ) G10 Raf2_2 0.12 0.88 سبز ( Green ) G30 Ham2_ 2 0.60 0.40 مختلط ( Mixed ) G11 Raf2_3 0.44 0.56 مختلط ( Mixed ) G31 Ham2_ 3 0.73 0.27 قرمز ( Red ) G12 Raf2_4 0.19 0.81 سبز ( Green ) G32 Ham2_ 4 0.73 0.27 قرمز ( Red ) G13 Far-1 0.40 0.60 مختلط ( Mixed ) G33 Gha-1 0.35 0.65 مختلط ( Mixed ) G14 Far-2 0.53 0.47 مختلط ( Mixed ) G34 Gha-2 0.53 0.47 مختلط ( Mixed ) G15 Far-3 0.39 0.61 مختلط ( Mixed ) G35 Gha-3 0.40 0.61 مختلط ( Mixed ) G16 Far-4 0.38 0.63 مختلط ( Mixed ) G36 Gha-4 0.58 0.43 مختلط ( Mixed ) G17 Dam-1 0.14 0.86 سبز ( Green ) G37 Kho-1 0.83 0.17 قرمز ( Red ) G18 Dam-2 0.18 0.82 سبز ( Green ) G38 Kho-2 0.90 0.10 قرمز ( Red ) G19 Dam-3 0.27 0.73 سبز ( Green ) G39Kho-3 0.86 0.14 قرمز( Red ) G20 Dam-4 0.07 0.93 سبز ( Green ) G40Kho-4 0.86 0.14 قرمز (GA) - 5′ UBC812 45 3′ - G 7 (CA) - 5′ UBC818 46 3′ - T 8 (AG) - 5′ UBC807 60 3′ - T 8 (AC) - 5′ UBC825 50 3′ - T 10 (AG) - 5′ A7 48 3′ - CC 6 (GT) - 5′ A13 40 3′ - YG 8 (AC) - 5′ UBC857 43 3′ - YT 8 (GA) - 5′ UBC840 56 3′ - CG 8 (GT) - 5′ UBC849 60 3′ - 5 CAg) ) - 5′ CAG5 57 3′ - RG 8 CA) ) - 5′ UBC848 48 3′ - T 8 (GA) - 5′ UBC810 R = A/ ...
Objective Ajowan (Trachyspermum copticum) is a medicinal species that is very useful and is used to treat stomach problems and some other diseases. This study was aimed to fingerprint Ajowan accessions which collected from different geographical regions of Iran by using ISSR markers and identify markers linked with agro-morphological traits through association mapping approach. Materials and methods In this study, number of 40 Ajowan genotypes related to 10 different populations from different regions of Iran were collected and then their morphological characteristics were recorded in greenhouse condition. Leaf samples were taken from each genotypes and ISSR fingerprinting was done after DNA extraction. Results The results of descriptive statistics indicate the existence of genetic diversity in the germplasm of the studied Ajowan in terms of morphological characteristics and the highest and lowest
... Genetic diversity is an essential element for genetic improvement, preserving populations, evolution and adapting to variable environmental situations [20,17]. On the other hands, determination of gene polymorphism is important in organism breeding [21,22] in order to define their genotypes and their associations with productive, reproductive and economic traits [23,24,25]. In this context, the present study was done to identify FAW strain(s) that feed on rice through molecular approaches. ...
The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), is an invasive insect pest of India native to the Western Hemisphere. The pest damages more than 350 plant species. FAW is genetically divided into two strains viz. corn (C) strain which feeds mostly on maize, sorghum, etc. and the other is a rice (R) strain that prefers rice and other small grasses. In the present study, fall armyworm samples were collected from rice crop in two different places of Tamil Nadu, India during 2019-20 and strain identity was confirmed. Polymerase Chain Reaction (PCR)- Restriction Fragment Length Polymorphism (RFLP) profile of mitochondrial cytochrome oxidase subunit I fragment confirmed the presence of both ‘R’ and ‘C’ strains of FAW in rice crop. Nucleotide variations were observed from PBS, TNAU isolate at five places and two places in Killikulam isolate. Phylogenetic analysis revealed that PBS, TNAU isolate ON247930 (C strain) has completely diverged from Killikulam isolate OM491244 (R strain).
... On the other hand, genetic study in indigenous breeds is a major concern considering the necessity of preserving what may be a precious and irreplaceable richness, regarding new productive demands [20]. Conservation should be based on a deep knowledge of the genetic resources of the specific breed [21]. Therefore, it is important to try to characterize genetically indigenous breeds [22,23]. ...
A survey on Drosophila was conducted from October 2018 to March 2019 (winter to early summer).
Drosophila’s were collected from 15 different localities of Ballari. Bottle trapping method and net sweeping
methods were employed for the collection of fruit flies. The collected fruit flies were cultured in culture bottles
containing wheat cream agar medium. A total of 733 Drosophila’s were collected amongst which 260
were males and 473 were females. The current study revealed that a total of 08 species were identified.
D. melanogaster and D. ananassae were found to be common in all the fifteen regions suggesting their
dominance in Ballari. (North – East part of Karnataka). The study reveals that not only the number of
Drosophila species varies among different places; but also the number of individuals belonging to same species
differs among different places under study. In the present study, consideration of the common and abundant
species shows that numerical variation exists in regard to these species at all fifteen altitudes.
Keywords: Cinderella of genetics; fruit fly; habitat; diversity; genome.
... The ability of the genetic assignment of individual members to a target breed is essential to the success of the conservation initiatives. It should be based on in-depth knowledge of the genetic resources of the specific breed [3]. Therefore, it is important to genetically characterize indigenous breeds using the recent advantages of molecular marker techniques. ...
This study analyzed the genetic diversity and structure of two Bulgarian indigenous sheep (Ovis aries) breeds – Kotel and Teteven, each presented by 4 flocks, using 15 microsatellite markers. A total of 195 alleles were identified. Among the markers used, the most informative were INRA5 and OarFCB20 with PIC values of 0.87. Both breeds showed a high level of genetic diversity with average values of He and Ho, respectively 0.74 and 0.76. The observed high level of genetic diversity is combined with the absence of heterozygous deficiency reported as Fis values of 0.04 and 0.07, respectively for Kotel and Teteven breeds. Low level of genetic differentiation between the two breeds was observed, as evidenced by the low value of Fst of 0.09, and analysis of variance (ANOVA) data showing that only 9% of the total variation is due to variation between breeds, whereas 91% is due to variation within breeds. Furthermore, we revealed a breeding practice that comprises an exchange of animals between the breeds which reflects in the clustering obtained by STRUCTURE analysis. According to it, Kotel breed is a more homogenous population and forms cluster 1, whereas Teteven breed is more heterogenous and consists of two subpopulations that form two distinct clusters. The results obtained in the present study confirm the high potential of microsatellite markers in studies related to both breed affiliation and purity and can serve as a basis for the implementation of future management and conservation programs of these indigenous breeds.
... Kermani is a meat and wool type, fat-tailed, medium-sized and white-wool sheep breed, indigenous to the southeastern areas of Iran and appropriately adapted to the unfavorable climatic conditions and pastures of low quantity and quality which is prevalent in the region (Mohammadabadi et al. 2017). The wool of Kermani sheep is fairly thick with a carpet grade. ...
... Zamani et al. (2011) reported percentages of ISSR primer polymorphism ranging from 69 to 77% by studying genetic diversity in the Mehraban Iranian sheep breed. Similarly Mohammadabadi et al., 2017 found 80.6% and 85.7% ISSR polymorphic loci for two primers used for characterization of the Kermani sheep breed in Iran. The high level of polymorphism shows that the markers used in this study are very informative and allow an unbiased estimation of the genetic variability in the studied populations. ...
Inter simple sequence repeat (ISSR) amplification was used to study the genetic diversity between three populations of the Sicilian-Sardinian dairy sheep breed. This breed is only found in the north of Tunisia (Beja and Bizerte governorates) where the climate is subhumid (> 600 mm / year) and is favorable to large forage production. The studied animals belong to three regions: Gnadil (Beja), Nagachia (Beja) and Fretissa (Bizerte). In total, 153 bands were amplified and all were polymorphic (100%). Within populations, the Nei’s gene diversity, the Shannon index and the percentage of polymorphic loci were between 0.08 and 0.16, 0.13 and 0.27 and 30.72% and 77.78% respectively. The coefficient of gene differentiation (Gst) and the gene flow (Nm) between populations varied from 0.12-0.2 and 1.99-3.65. The UPGMA dendrogram, grouping the three studied populations, based on the Nei’s standard genetic distances showed that the populations of Nagachia and Fretissa are genetically the closest while the population of Gnadil is the most distant one.
... The application of molecular genetics in animal husbandry has many important advantages (Khodabakhshzadeh et al., 2016;Zamani, Akhondi, & Mohammadabadi, 2015). One such significant advantage is the genotyping of individuals for specific genetic loci known to be associated with phenotypic traits of relevance to cattle farming and breeding (Khodabakhshzadeh et al., 2016;Mohammadreza Esfandyarpoo, & Mousapour, 2017). Often all the genes that affect a polygenic trait are not precisely known, although a number of candidate genes with major effects have been recognized . ...
... Genetic diversity in indigenous breeds is a major concern considering the necessity of preserving what may be a precious and irreplaceable richness, regarding future productive demands (Khodabakhshzadeh et al., 2016). Conservation should be based on a deep knowledge of the genetic resources of the specific breed (Mohammadreza et al., 2017;Zamani et al., 2015). Therefore, it is important to characterize genetically indigenous breeds. ...
Max dimerization protein 3 (MXD3) belongs to the MYC superfamily of basic helix‐loop‐helix leucine zipper transcription factors, and MXD3‐MAX heterodimers can bind to promoters of target genes to modulate their expression. The aim of this study was to determine the MXD3 mRNA expression levels in various cattle tissues comprising heart, liver, spleen, lung, kidney, Longissimus dorsi muscle and subcutaneous fat in Chinese Qinchuan and Xianan cattle breeds. The RT‐qPCR data showed that the MXD3 gene was variably expressed between all tissues and at levels that were significantly different between two breeds (p < .05). We used the polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) method to investigate the possible association between single‐nucleotide polymorphisms (SNP) within the MXD3 gene and five different growth traits in cattle. We found two intronic SNPs (g.2694 C>T and g.3801 T>C) and one SNP in 3′untranslated region (3′UTR) (g.6263 G>A) of MXD3 gene. Association analysis revealed strong associations between pairwise and triple SNP combinations and the growth traits. Based on these results, we suggest that MXD3 polymorphisms could be useful as molecular markers in the Chinese beef cattle breeding program.
... Some studies have shown that positive selection of essential genes in goat breeds may be associated with reproduction, conformation, behavior, and resistance to diseases and parasites [9]. Determination of gene polymorphism is important in farm animal breeding [10], as it helps to define the genotypes of animals and their associations with productive, reproductive and economic traits. In recent years, the utilization of indels (insertion/deletion) has become more common in MAS studies [11]. ...
The down syndrome cell adhesion molecule like 1 (DSCAML1), is associated with the development of the nervous system and neurologic diseases. Previous Genome-wide association studies have shown that it is associated with sperm morphology, suggesting it has a critical role in fecundity. In this study, expression profiles of goat DSCAML1 mRNA were analyzed. The results showed that its expression in the testis differ significantly between the mitotic stage and meiotic stage. Three insertion/deletion (indel) variants of goat DSCAML1 were determined in the Shaanbei White Cashmere Goat (SWCG, n = 2162). Based on the association analysis, two indels (P2-16bp, P14-15bp) were significantly related to sperm quality (sperm motility and sperm density) in male goat and three loci were markedly related to the first-birth litter size in female goat (P = 4.0 × 10-6; P = 1.0 × 10-6; P = 4.7 × 10-2). In male goats, the different genotypes of P2-16bp and P14-15bp revealed a noticeable effect on the expression of DSCAML1. Moreover, the effects observed in the first-birth litter followed a similar trend, which may provide the basis for further research of DSCAML1 gene function and marker assisted selection (MAS) programs to improve reproductive traits.
