Christopher U Orji1*, Ignatius O Onyeocha2, Steven S Shaida3, Peter M Dede4, Bitrus Yakubu5, Elijah E Ella6 and Pam D Luka5
...a were used to calculate haplotype, haplotype diversity and nucleotide diversity for the two species. Based on combined loci of cytochrome oxidase II (COII) and cytochrome b (CytB), twelve haplotypes were generated for G. p. palpalis and five for G. m. submorsitans. Similarly, for the combined loci, haplotype diversity (Hd) was higher for <...
Pan-pan Guo1, Wei Liu2, Yan Li2, Rui-yu Ma2, Wang Zaigui1*, Kai Zhan2*, Jun-ying Li2 and Sheng-nan Liu2
.... Additionally, four HTT haplotypes (H1: GG; H2: GC; H3: AG; H4: AC) and their frequency distributions were estimated using the phase program. Haplotypes combinations constructed on these two SNPs of HTT gene were associated with some reproduction traits. In particular, diplotype H1H1 had positive effect on reproduction traits, diplotype H2H4 had negative effect of reproduction traits. In conclusion, our study showed that po...
Lingtong Ye1, Chao Cao1,2, Bin Tang1,2, Tuo Yao1, Ruixuan Wang1 and Jiangyong Wang1*
...me larvae share the same haplotypes as adults. These findings clearly indicate that the larvae collected from sea waters around an oyster farm belong to P. websteri, the same species as the adult worms collected from the oyster Crassostrea hongkongensis in that locality. Two polydorid-specific primers were successfully designed, for the first time, to amplify target fragments of the COI gene. This study is the first to molecularly validate uniden...
Jun Gao1,2, Liang-Liang Yue3, Xianhuan Jiang1, Liju Ni4, Muhammad Aqeel Ashraf5, Yuxun Zhou,1 Kai Li1,* and Junhua Xiao1,*
...R) were sequenced and 49 haplotypes were observed. No shared haplotype was found among different geographic populations. High Fst values among the populations suggested that fragmentation of habitat has resulted in genetically distinct populations. The trees, inferred from maximum likelihood and Bayesian phylogenetic analysis, highly supported all the M. fortis individuals clustering into one monophy...
Wang-Dui Basang1, Tian-Wu An2, Luo-Bu Danjiu3, Yan-Bin Zhu1, Shi-Cheng He3, Xiao-Lin Luo2, Wei-Wei Ni4, Xiao Wang4, Shu-Zhu Cheng4, Jian Wang4 and Guang-Xin E4,*
... number variants, and 59 haplotypes were detected. The number of haplotypes within the population ranged from 17 (SN and JL) to 28 (DX). The haplotype diversity ranged from 0.9420 (SN) to 0.9770 (NR). The highest nucleotide diversity was found in the JL population (0.01479), whereas the lowest was found in the SN (0.00894) population. Phylogenetic analysis revealed that these four populati...
Yuan Li1, Liyan Zhang2, Karhoe Loh3, Ji Feng1, Xinqing Zheng1, Puqing Song1 and Longshan Lin1,*
... moderate, and two major haplotype lineages were detected that were differentiated approximately 0.3 million years ago. These two haplotype lineages differed significantly in frequency distribution of Chinese and Malaysian populations, showing an imperfect geographical pedigree structure. Results of AMOVA also showed that the genetic differentiation was mainly among populations. According to the distribution of the
Fehmeeda Fatima, Asif Nadeem* and Maryam Javed
...ted. The total number of haplotypes (h) was found to be 17 and haplotype diversity (Hd) was 0.862. Nucleotide diversity (pi) was calculated to be 0.00210 and Tajima’s D neutrality test for neutral mutation indicated a negative value. Moreover, the results of homology analysis showed maximum similarity with sequences of goat and sheep sequences (partial) and were found to be 99.93% and 99.35%, respectively which ...
Aiguo Zhou1,3,4, Shaolin Xie1,4, Zhenlu Wang1, Lanfen Fan1, Yanfeng Chen2, QiaoYe1, Fang Zeng1 and Jixing Zou1,*
... 0.000 to 0.002. For the haplotypes of two color morphs of Channa argus, the mean pair-wise genetic distances were estimated as 0.002, which were within the intra-species genetic distance interval for Channa species, indicating that they belonged to the same species, but not subspecies at the molecular level. Moreover, take Lateolabrax maculates and Epinephelus coioides as outgroups, molecular phylogenetic tree showed that all the h...
Faiz Muhammad1,2, Canfeng Dou1, Zhen-ming Lü1,*, Li Gong1, Xun Du1 and Muhammad Shafi3
...subunit ATPase 6, thirty haplotypes and 140 polymorphic sites were noted, whereas (0.740, 0.048) high and low haplotype and nucleotide diversity observed. The data was further tested with AMOVA that validates 91.24% variation among populations and 8.76% within population. Genetic fixation index was also calculated as 0.91243*. The neighbor-joining phylogenetic analysis revealed three lineages. The Dongshan population di...
Liyan Zhang1,2, Zhidong Zhou1,3, Haiping Li1,2, Yanlong Qiao4, 5 and Yueping Zhang1,3,*
...or-joining (NJ) tree and haplotype network analyses, and gene flow and exact P test results revealed that a wide range of gene flow occurred among the four S. japonicus populations. Analysis of molecular variance (AMOVA) and Fst analysis showed that genetic variation was mainly derived from within populations, and genetic divergence was very weak among populations. The complex hydrologic environment of the Taiwan Strait and its ...
Zhen-Yang Wu1, Guang-Xin E2,*, Hui Ran1, Da-Hui Wang1 and Tian-You Yang1
...nformative sites, and 18 haplotypes were detected. The number of haplotypes within populations ranged from one (WS and DJ) to six (JK). Haplotype diversity ranged from 0.000 (DJ and WS) to 0.793 (JK). The largest amount of nucleotide diversity was found in the SQ population (0.03111 ), whereas the smallest amount was in the DJ and WS (0.00000) populations. Phylogenetic analysis revealed th...
Zhaochao Deng1, Jingchen Chen1, Na Song2, Yongzhen Li3 and Zhiqiang Han1,*
...were obtained defining 7 haplotypes in the South China Sea population. Contrary to heterogeneous expectation, AMOVA and pairwise FST values showed that the genetic differences in this region were all non-significant. The pattern of population demography showed a stable model in this species in the South China Sea population. To reveal its population structure within the large-scale geography distribution, we added 169 sequences of the mitocho...
Zhaochao Deng1, Na Song2, Yongzhen Li3, Tianxiang Gao1 and Zhiqiang Han1,*
...ere obtained defining 39 haplotypes. Based on the NJ tree, two distinct lineages were detected, with strong frequency differences in the geographical distribution. Both lineages were found in Xisha and Zhongsha archipelagos, but only one lineage (lineage B) was detected in Nansha archipelago. Contrary to homogenization expectation, AMOVA and pairwise FST values showed that the genetic differences among three archipelagos were all significant....
SiRui Wang1,2, Fekede Regasa Joka1,2, XiaoLong Wang1,2,* and SuYing Bai2,*
...d by PCR sequencing. The haplotypes were analysed by DNA SP software. The Datamonkey Adaptive Evolution Server was used to detect the selection pressure. Phylogenetic analyses of the reported sequences of jungle fowl (Gallus gallus) and the 10 tested birds were performed. A total of 10 nucleotide sequences of the GED region of the Mx gene in wild birds were obtained, with a length of 231 bp, encoding 77 amino acids. The third locus in all tested ...
Bingbing Gao1, Na Song1, Zhonglu Li2, Tianxiang Gao3 and Liqin Liu3,*
... 26 mutation loci and 27 haplotypes were detected. All six populations were characterized by low haplotype diversity (0.39–0.59) and low nucleotide diversity (0.00038–0.00073). The result of AMOVA and pairwise Fst values indicated weak or no genetic differentiation among different populations. Haplotype network and NJ phylogenetic trees revealed that there was...
Shanshan Cai1, Tianxiang Gao2, Binlun Yan3, Aiyi Zhu1 and Xiumei Zhang1,2,*
...e excluded for no shared haplotype with broodstock. Further 81 (14.81%) crabs were identified as hatchery-reared individuals based on microsatellite loci from the remaining 305 crabs. Our results also showed high genetic diversity and a certain degree of heterozygote deficiency of natural swimming crab populations. The advancing technology and its unique advantages will make molecular markers as novel and highly-efficient approaches for assessment of stock enh...
Tasleem Akhtar1,2,Ghazanfar Ali1,*, Nuzhat Shafi2 and Abdul Rauf2
...m 1527 to 1552 bps. Five haplotypes (h) were observed, with haplotype diversity (Hd) 0.5323±0.080. Among 5 haplotypes, 2, 2 and 1 haplotype were detected in S. plagiostomus, S. niger and S. esocinus, respectively. Haplotype diversity was lowest and same in S. esocinus, S. niger and S. pro...
Peng Ren1, Xian-Qing Liu1, Chao-Wu Yang2,3, Hua-Rui Du2,3, Xiao-Song Jiang2,3 and Yi-Ping Liu1*
...rences were found in the haplotypes of SNP1 and SNP2 (P>0.05). These results suggest that SNP4 (A4812316G) in the 3’-UTR of the MyD88 gene is linked to genetic resistance to Salmonella Pullorum infection and may provide an important reference for the marker-assisted selection of chickens during disease-resistance breeding.
...
Muhammad Younis Laghari1,2, Zixia Zhao1, Yiwen Gong3, Punhal Lashari1,2, Shangqi Li1, Jian Xu1 , Ateeque Rahman Khooharo4, Jiongtang Li1,* and Yan Zhang1*
...lymorphic, including six haplotypes with an average sequence divergence of 11.03% (SE = 0.78%). Four haplotypes (MF177501-MF177504) were shared in these four population. However, two specific haplotypes (MF177499-MF177500) were only observed in Hainan population. To simplify procedure and improve effectiveness of identifying the Hainan population, one specific PCR-based marker acted as IND...
Jiantong Feng, Xueping Wen, Yahong Guo, Yingying Ye*, Jiji Li and Baoying Guo
...Results revealed that 33 haplotypes were defined in COIII gene, and 30 haplotypes were defined in 12S rRNA gene. The pairwise Fst values between the ZS population and other four populations were range from 0.122~0.154 (COIII, P< 0.05) and 0.052~0.228 (12S rRNA, P<0.05), respectively. The revealed that ZS population was significant divergence from other four populations, and no significan...
Peimin Yang*, Zongyun Hu, Yixin Liu, Guanghai Jin and Lei Wang
...polymorphic sites and 20 haplotypes among five populations, and the samples exhibited high haplotype diversity (h=0.8467) and low nucleotide diversity (Pi=0.0063). Genetic distances ranged from 0.0002 to 0.0149 within and 0.0007 to 0.0140 between populations. AMOVA analysis indicated significant genetic differentiation among populations (Fst=0.3202, P<0.01) and 68.98% of t...
Guang-Hui Tan, Yi-Yu Zhang*, Yuan-Yu Qin, Lei Wu and Jie-Zhang Li
...ity, respectively. Three haplotypes and six diplotypes were identified by the combination of two SNPs. Diplotypes had dominantly affected on tested lipid indexes except for IMF. Diplotype H1H1 was advantageous for the improvement of meat quality. Therefore, our data suggested that two novel SNPs: CDS 216 A>G and CDS 681 T>A in CYP7A1 gene were potential candidate markers for improving meat quality. It also provides reference data for early breeding and s...
Yan Zhou1,2, Hai Xia Han1,2, Qiu Xia Lei1,2, Jin Bo Gao1,2, Wei Liu1,2, Fu Wei Li1,2, Jie Liu1,2 and Ding Guo Cao1,2*
...duction in chickens, the haplotypes and diplotypes based on three genetic mutations (NC_006127.2:g.8467G>A, NC_006127.2:g.12321G>A and NC_006127.2:g.13876A>G) were constructed, and the associations of diplotypes with reproduction traits were assessed, their effects on gene expression were evaluated also. As a result, three haplotypes H1 (G-G-A), H2 (G-G-G) and H3 (A-A-G) were obtained, H1 was the main
Sehrish Firyal1,*, Ali Raza Awan1, Muhammad Umair Latif1, Muhammad Tayyab1, Muhammad Wasim1, Shagufta Saeed1 and Imaad Rashid2
...athy pigeon. Cytb haplotype for local domestic breed was developed. Homology analysis of Cytb gene revealed Columbia livia as closest homologue of Pakistani Lathy pigeon with five novel SNPs. Phylogenetic analysis of domestic lathy pigeon indicated the monophyletic relation with C. livia. We are reporting for the first time, the novel SNPs in the Cytb gene of local domestic pigeon breed that might act as panel of molecular ma...
Muhammad Umer Khan1,2*, Muhammad Farooq Sabar1, Atif Amin Baig3, Arif-un-Nisa Naqvi4 and Muhammad Usman Ghani1
... A total of 75 different haplotypes were identified in Shin people; among them, 72 were unique and 3 were shared by more than one individual. This study revealed the predominance of West Eurasian lineages in the Shin population (59.49%), followed by South Asian lineages (25.32%) and then East and Southeast Asian lineages (15.19%). Shin population presented a high genetic diversity of 0.9996 and a low random match probability of 0.0129. To the best of our knowl...
Ehsan Kashani1, Hamid Reza Rezaei2*, Morteza Naderi3 and Nematolah Khorasani4
...lades without any common haplotypes. Long-eared specimens grouped in two distinct phylogenetic groups which belong to two different geographic areas while for P. hypomelas no significant divergence happened in the species life history.
...
Shuanping Zhao, Lei Xu, Hai Jin and Yutang Jia*
... total of four different haplotypes were constructed and the frequency of the main haplotypes AAG accounted for over 61.2 % of the total individuals. Association analysis indicated that all of the three SNPs were significantly associated with growth traits in the detected population. Furthermore, real-time PCR indicated that CFL2 mRNA was varied expressed in all studied tissues. The results of our study provide eviden...
Yongyun Zhang1, 2, Xinyang Fan1, Fangting Zhou1, Weizhen Li3, Yina Ouyang1,4 and Yongwang Miao1*
...ht buffalo CSN1S1 haplotypes were defined in this study, and accordingly, 6 protein variants and 2 synonymous variants of αS1-CN were inferred and named. The variants A, B’, B’’, C, E and F were observed only in river buffalo, whereas variant D was found only in swamp buffalo. The variant B was shared by both types of buffalo with high frequencies. The buffalo variants determined here did not exist in Bos...
Aiguo Zhou1,2, Di Sun1,2,Shulin Liu 1,2, Yongyong Feng1,2, Yue Zhang3,
Yanfeng Chen4, Shaolin Xie1,2* and Jixing Zou1,2*
...wed that there were nine haplotypes in 60 individuals, which were eight unique and one shared haplotypes. In addition, the genetic distance for inter-species of all the haplotypes ranged from 0.000 to 0.004. And the mean pair-wise genetic distance between the two color morphs were estimated to be 0.001. This indicated that the “Bicolor” and “White” types of northern...
Xuhai Wang1,2, Xin Li1, Fangyuan Yuan1, Chaocheng Li1, Bin Jia1* and Song Jiang1*
...nt and non-resistant MHC haplotypes after oral infection with E. granulosus eggs. The results demonstrated that miR-216b negatively regulated IL2RB in the cystic echinococcosis intestinal tissues, and they were differentially expressed in the intestine tissue between the resistant sheep and non-resistant sheep, more widely distributed in the resistant group. These results illustrated that miR-216b and IL2RB activated stronger immune response in the resi...
Yahong Guo1,3, Zeqin Fu1,3, Jiantong Feng1,3, Chengrui Yan1,3, Yingying Ye1,3*, Kaida Xu2 and Baoying Guo1,3
... The results showed that haplotype diversity (h) of the cultured specimens groups (from 0.621 to 0.797; average, 0.717) was higher than that of three wild specimens groups (ZSW, WZW, and NNW; from 0.428 to 0.668; average, 0.560). The pairwise FST values suggested that only the FZW sample showed significant divergence from the others. The wild and cultured ZS and WZ specimens groups were similar, and the wild and cultured ND specimens g...
Xiaoyun He1, Yongfu La2, Jinxin Wang1, Ran Di1, Qiuyue Liu1, Xiangyu Wang1, Wenping Hu1 and Mingxing Chu1*
...lt;0.01). The results of haplotypes analysis indicated that H2, H7 were preponderant haplotype in high prolificacy sheep breed. The litter size of TT genotype was significantly higher than that in CC genotype at T1235C loci in STH sheep (P<0.05). The current study provides evidence in sheep for genetic markers that might be used in breeding program.
...
Shahid Sherzada1,2*, Muhammad Naeem Khan1 and Masroor Ellahi Babar2
... polymorphic sites and 4 haplotypes. Mean haplotypes and nucleotide diversity was 0.42 and 0.0018, respectively. The mean intraspecific and intragenric K2P genetic distances were 0.2% and 1.2%, respectively. Rate of transitional and transversional substitution was 16.68% and 4.16%, respectively. The transition/transversion bias value R was 1.25. The negative values of Tajima D test as well as Fu and Li D and F tests supporte...
Asli Salcioglu
...base. The results of the haplotype network and phylogenetic trees show three distinct Spicara haplotypes/haplogroups, corresponding to three different species. Additionally, the number of mutations and high values of sequence divergences were useful in differentiating the three different Spicara....
Abida Shehzadi*, Muhammad Shafique and Ahmad Ali Shahid
...rt tandem repeat (Y-STR) haplotype diversity analysis of 143 healthy unrelated male individuals from Jat population of Pakistan. Seventeen Y-STR loci were simultaneously amplified through AmpFISTR®YfilerTM PCR amplification kit. Evaluation of statistical parameters for forensic importance revealed in recognition of 124 unique haplotypes with diversity value of 0.996. Locus DYS385a/b demonstrated highest power of discrimi...
Weidong Huang1,2,3, Xinyue Liang1,2,3, Xiufeng Xie4, Xingmin Wang2, 3 and Xiaosheng Chen1,2,3*
...o showed a high level of haplotype diversity (Hd = 0.902) and the low level of nucleotide diversity (Pi = 0.004). In addition, the number of haplotypes was 17 and the same elytral color patterns of M. sexmaculatus didn’t share the same haplotype. Furthermore, phylogenetic analyses showed all M. sexmaculatus samples formed a single clade, but the identical elytral pattern individuals ...
Ngoc Tan Nguyen1*, Minh Thanh Tram1, Thi Thu Pham1, Tan Loi Le1, Thi Khanh Ly Nguyen1, Tuan Thanh Hoang2, Cong Thieu Pham3, Nguyen Khang Duong4
...nucleotide polymorphism, haplotype diversity and genetic distance to construct a phylogram. Results showed that the fragment of 687 bp was successfully amplified. Examination of 49 sequence variants in 599 bp of the control region revealed the nucleotide composition was Adenine (A) = 32.55%, Thymine (T) = 28.33%, Guanine (G) = 14.67%, Cytosine (C) = 24.87% and G+C content was 39.12%. Out of a total of 50 nucleotide polymorphic sites, 48 were transition and 2 w...
Ngoc Tan Nguyen1*, Pham Kim Ngan Nguyen1, Thao Huong Phan1, Tan Loi Le1, Thi Khanh Ly Nguyen1, Tuan Thanh Hoang2, Cong Thieu Pham3, Cong Dinh Nguyen3, Nguyen Khang Duong4
...polymorphic sites and 26 haplotypes were observed. Nucleotide and haplotype diversity index (π and Hd) were 0.06267 and 0.987, respectively. Genetic distance among swamp buffalo populations was smaller (ranging 0.050-0.056) than between Murrah and the swamp buffalo populations (ranging 0.091-0.125). Among the three native Vietnamese buffalo groups, the genetic distance between Bao Yen and LangBiang (0.050) buffalo populat...
He-Cai Zhang, Tian-Ge Hu, Chang-Ying Shi, Guang-Wen Chen* and De-Zeng Liu
...e results showed that 46 haplotypes were detected in total, including 10 shared haplotypes and 36 private ones. The overall haplotype diversity (Hd) and nucleotide diversity (π) were 0.961 and 0.00157, respectively. The phylogenetic relationship and haplotype network analysis indicated that there was no obvious correspondence between the
Muhammad Salman Ikram1, Tahir Mehmood1,2*, Sehrish Firyal3, Huma Sattar4, Shagufta Saeed3, Fareeha Nadeem3 and Muhammad Imran Mahmood Khan5
...Y-STR in relation of its haplotype diversity and frequencies among different population, role of paternal lineages identification which helps to determine the mutation rate of Y-STR and its relationship with paternal lineages determination. When familial searching is coupled with genealogy inquiry, the review article will help us comprehend the combined use of Y-chromosome information and family information and understand the cases on the basis of specific for...
Nasir Ali1,2,6, Muhammad Ilyas2,3, Nazia Akbar1,2*, Gohar Rahman2, Shakirullah Khan4, Mujaddad Ur Rehman6, Abdul Samad5, Habib Ahmad1,2 and Bibi Nazia Murtaza7*
...ults revealed 25% unique haplotypes in ancient samples whereas 28% unique haplotypes have been observed in the modern samples. The most frequent haplotype found was H2a (23% in ancient and 10% in modern samples). Our results show that with the exception of ancient Dir, there are genetic similarities among the ancient lines between Hazara, Chitral and Swat. It revealed that most of the anci...
Weidong Liu, Jiashen Tian, Zhen Wang, Zhongren Kong, Jiabo Han and Zhichuang Lu*
... population in 2005. The haplotype diversity of Liaodong Gulf spotted seals was low compared to other spotted seal populations in other habitats. Fortunately, the genetic diversity of the current Liaodong Gulf spotted seal population was higher than 15 years ago, and the population expanded between 2005 and 2020. Our findings indicated that conservation activities for Liaodong Gulf spotted seals in recent decades have been valuable, and should persist in the f...
Perinçek Seçkinozan Seker
...otide diversity and high haplotype diversity. A total of two haplotypes were identified for cyt b, while three haplotypes were identified for COI. Of the haplotypes detected, two cyt b and two COI haplotypes were specific to Turkey. Molecular phylogenetic analyses; Maximum Likelihood (ML), Bayesian Inference (BI), and ...
Chengrui Yan1, Jing Miao1, Jiantong Feng1, Liping Xia1, Yingying Ye1,2*, Jiji Li1 and Baoying Guo1,2
... and demographic (AMOVA, haplotype networks and mismatch distribution) revealed a single genealogical branch and indicated undifferentiation of T. clavigera in the China Sea. Migration dynamic analysis showed that gene flow was asymmetrical and QD as the source population. Additional, canonical correspondence analysis (CCA) analysis between environmental factors (SKT, TOP, SLP, and SUND) and haplotypes indicated that SLP and...
Iqra Almas, Samia Afzal*, Muhammad Idrees, Muhammad Shahid, Iram Amin and Kausar Malik
...ere shown more number of haplotypes and total diversity as compared to sons. The quasispecies analysis showed the mother and sons were infected with HBV having similar genetic makeup, indicating the vertical transfer of infection. This case study provides knowledge about genetic variations that contributes to the improved diagnosis of the infection, treatment therapy, follow-up, and future treatment strategies....
Rongrong Wang1,2, Da Ji1,2, Junjie Yao1,2*, Wenzheng Zhang1,2, Xianjun Zhou1,2, Xin Su1,2 and Tianquan Bai3
...dividuals displayed four haplotypes, and the overall haplotype diversity (Hd) and nucleotide diversity (Pi) of the three C. sowerbyi groups were 0.531 and 0.00067, respectively. Analysis of molecular variance (AMOVA) showed that inter- and intrapopulation variation accounted for 41.63039% and 58.36961%, respectively, of the total variation, and the genetic variation coefficient (Fst) was 0.05268. The gene flow (Nm) values be...
Nguyen Ba Trung1,2*, Pham Thi Kim Phuong1,2
... the Bos indicus type I1 haplotype, suggesting relatively high genetic diversity in the maternal lineage. The sequence analysis of the SRY gene suggests that all the males possess a zebu-type haplotype, which may be derived from a cross between Bos javanicus and zebu. The results of the genotyping of the functional genes indicated that the NCAPG and DGAT1 genes are polymorphic, whereas the RNF212 gene is monomorphic. Particu...
Nguyen Ba Trung1,2*, Pham Thi Kim Phuong1,2
... the Bos indicus type I1 haplotype, which implies a significant level of genetic diversity within their maternal lineage. According to the SRY gene sequence study, all of the males have a zebu-type haplotype, which could have resulted from a hybrid between Bos javanicus and zebu. Based on the genotyping analysis of the functional genes, the DGAT1 gene exhibits polymorphism, whereas the NCAPG and RNF212 genes display monomorp...
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