Genetic Linkage
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2022 ◽  
Vol 12 ◽  
Xinxiu Yu ◽  
Rajesh Joshi ◽  
Hans Magnus Gjøen ◽  
Zhenming Lv ◽  
Matthew Kent

Consensus and sex-specific genetic linkage maps for large yellow croaker (Larimichthys crocea) were constructed using samples from an F1 family produced by crossing a Daiqu female and a Mindong male. A total of 20,147 single nucleotide polymorphisms (SNPs) by restriction site associated DNA sequencing were assigned to 24 linkage groups (LGs). The total length of the consensus map was 1757.4 centimorgan (cM) with an average marker interval of 0.09 cM. The total length of female and male linkage map was 1533.1 cM and 1279.2 cM, respectively. The average female-to-male map length ratio was 1.2 ± 0.23. Collapsed markers in the genetic maps were re-ordered according to their relative positions in the ASM435267v1 genome assembly to produce integrated genetic linkage maps with 9885 SNPs distributed across the 24 LGs. The recombination pattern of most LGs showed sigmoidal patterns of recombination, with higher recombination in the middle and suppressed recombination at both ends, which corresponds with the presence of sub-telocentric and acrocentric chromosomes in the species. The average recombination rate in the integrated female and male maps was respectively 3.55 cM/Mb and 3.05 cM/Mb. In most LGs, higher recombination rates were found in the integrated female map, compared to the male map, except in LG12, LG16, LG21, LG22, and LG24. Recombination rate profiles within each LG differed between the male and the female, with distinct regions indicating potential recombination hotspots. Separate quantitative trait loci (QTL) and association analyses for growth related traits in 6 months fish were performed, however, no significant QTL was detected. The study indicates that there may be genetic differences between the two strains, which may have implications for the application of DNA-information in the further breeding schemes.

2022 ◽  
Vol 21 (1) ◽  
pp. 131-138
Yue YIN ◽  
Wei AN ◽  
Jian-hua ZHAO ◽  
Yan-long LI ◽  
Yun-fang FAN ◽  

Biology ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 50
Wei Cui ◽  
Da Huo ◽  
Shilin Liu ◽  
Lili Xing ◽  
Fang Su ◽  

Genetic linkage maps have become an indispensable tool for genetics and genomics research. Sea cucumber (Apostichopus japonicus), which is an economically important mariculture species in Asia, is an edible echinoderm with medicinal properties. In this study, the first SNP-based high-density genetic linkage map was constructed by sequencing 132 A. japonicus individuals (2 parents and 130 offspring) according to a genotyping-by-sequencing (GBS) method. The consensus map was 3181.54 cM long, with an average genetic distance of 0.52 cM. A total of 6144 SNPs were assigned to 22 linkage groups (LGs). A Pearson analysis and QTL mapping revealed the correlations among body weight, body length, and papillae number. An important growth-related candidate gene, protein still life, isoforms C/SIF type 2 (sif), was identified in LG18. The gene was significantly highly expressed during the larval developmental stages. Its encoded protein reportedly functions as a guanine nucleotide exchange factor. These results would facilitate the genetic analysis of growth traits and provide valuable genomic resources for the selection and breeding of new varieties of sea cucumbers with excellent production traits.

2021 ◽  
Vol 43 (3) ◽  
pp. 2276-2288
Lei Wang ◽  
Songpeng Jia ◽  
Yuxuan Zhang ◽  
Shuhong Jiang ◽  
Yuhan Chen ◽  

To provide the theoretical basis for researching growth, development, and molecular marker-assisted breeding of the economically important Yellow River carp (Cyprinus carpio haematopterus) using dynamic quantitative trait locus (QTL) mapping, we constructed three genetic linkage maps from 207 progeny using a new modified genotyping-by-sequencing method. The three maps contained 16,886, 16,548, and 7482 single nucleotide polymorphism markers, respectively, with an average interval of 0.36 cM, 0.45 cM, and 1.00 cM. We identified 148 QTLs related to four growth traits that were located on 25 chromosomes from three growth stages of Yellow River carp. A total of 32, 36, 43, and 37 QTLs were associated with body length, height, width, and weight, respectively. Among them, 47 QTLs were detected for only one growth trait in one stage, but all of the other QTLs were co-localized. Of the 14 main QTLs, 13 were located on chromosome 12, which suggests the presence of growth-related genes on this chromosome. We then detected 17 candidate genes within 50 K upstream and downstream of the 14 main QTLs. This is the first report of the dynamic QTL mapping of growth traits of Yellow River carp, and the results can be used in future studies of growth, development, and molecular-assisted breeding of this species.

2021 ◽  
Vol 2021 ◽  
pp. 1-6
Kiandokht Babolhavaeji ◽  
Leili Shokoohizadeh ◽  
Morteza Yavari ◽  
Abbas Moradi ◽  
Mohammad Yousef Alikhani

Background. The aims of the current study are the identification of O157 and non-O157 Shiga Toxin-Producing Escherichia coli (STEC) serogroups isolated from fresh raw beef meat samples in an industrial slaughterhouse, determination of antimicrobial resistance patterns, and genetic linkage of STEC isolates. Materials and Methods. A total of 110 beef samples were collected from the depth of the rump of cattle slaughtered at Hamadan industrial slaughterhouse. After detection of E. coli isolates, STEC strains were identified according to PCR for stx1, stx2, eaeA, and hlyA virulence genes, and STEC serogroups (O157 and non-O157) were identified by PCR. The genetic linkage of STEC isolates was analyzed by the ERIC- (Enterobacterial Repetitive Intergenic Consensus-) PCR method. The antimicrobial susceptibility of STEC isolates was detected by the disk diffusion method according to CLSI guidelines. Results. Among 110 collected beef samples, 77 (70%) were positive for E. coli. The prevalence of STEC in E. coli isolates was 8 (10.4%). The overall prevalence of O157 and non-O157 STEC isolates was 12.5% (one isolate) and 87.5% (7 isolates), respectively. The hemolysin gene was detected in 25% (2 isolates) of STEC strains. Evaluation of antibiotic resistance indicated that 100% of STEC isolates were resistant to ampicillin, ampicillin-sulbactam, amoxicillin-clavulanic acid, and cefazolin. Resistance to tetracycline and ciprofloxacin was detected in 62.5% and 12.5% of isolates, respectively. The analysis of the ERIC-PCR results showed five different ERIC types among the STEC isolates. Conclusion. The isolation of different clones STECs from beef and the presence of antibiotic-resistant isolates indicate that more attention should be paid to the hygiene of slaughterhouses.

Chinyere Charity Ezeanya-Bakpa ◽  
Nneka Regina Agbakoba ◽  
Charolette Blanche Oguejiofor ◽  
Ifeoma Bessie Enweani-Nwokelo

Background: Genetic evidence of asymptomatic Mycoplasma hominis (M. hominis) and Ureaplasma urealyticum (U. urealyticum) infection associated with infertility among females is lacking because suitable high throughput molecular methods have not been applied. Objective: This study aimed to explore the occurrence of M. hominis and U. urealyticum in the genital tract of females with asymptomatic infection and infertility as well as determine their genetic relatedness. Materials and Methods: The study group included 100 asymptomatic females and 31 females diagnosed with infertility. Sequencing of the 16S rRNA gene following DNA extraction was performed directly from endo-cervical swabs. Phylogenetic analysis established the genetic linkage between the isolates from both groups. Results: In asymptomatic females, M. hominis and U. urealyticum were detected with a prevalence of 8% and 2% respectively. Among females with infertility, the prevalence was 6.45% and 3.23% for M. hominis and U. urealyticum respectively. In both groups, M. hominis occurred significantly more frequently. Phylogenetic analysis revealed three distinct clusters in both groups: two with already characterized M. hominis and Ureaplasma species (28.6% of the overall Mycoplasma spp.) and one distinct cluster matched with U. urealyticum. Furthermore, all M. hominis from asymptomatic females clustered significantly with infertility contrary to U. urealyticum. The M. hominis cluster was significantly linked to two strains from China. Conclusion: The sequence analysis of Mycoplasma and Ureaplasma in the genital tract of asymptomatic and infertile females showed significant association; therefore, it is paramount to consider them as possible etiologic agents of infertility and genital infection, especially when the etiology of infertility is unknown. Key words: Mycoplasma hominis, Ureaplasma urealyticum, Genetic linkage, Asymptomatic infections, Infertility.

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