Genetic Basis of Cyprinid Herpes Virus-3 Resistance in Common Carp

The goal of this project was to provide scientific and technical basis for initiating the development of breeding protocols using marker assisted selection for viral disease resistance in common carp. The specific objectives were: 1) Establishing families and characterizing the phenotypic and genetic variation of viral resistance; 2) Measuring the dynamics of immune response and developing a method to measure the long term immune memory; 3) Developing markers and generating a new genetic linkage map, which will enable initial QTL mapping; and, 4) Identifying genetic linkage of markers and candidate genes (like MHC and TLRs) with resistance to CyHV-3. The common carp is an important farmed freshwater fish species in the world. Edible carp is second only to tilapia in Israeli aquaculture production and ornamental carp (koi) is an important product in both the US and Israel. Carp industries worldwide have recently suffered enormous economic damage due to a viral disease caused by Cyprinid herpes virus 3 (CyHV-3). Aside from preventative measures, a sustainable solution to this problem will be to establish a genetic improvement program of the resistance of fish to the pathogen. The aims of the project was to take the necessary first steps towards that. The differences in survival rates after infection with CyHV-3 virus among 20 families from six types of crosses between three carp lines (two commercial lines and one wild-type carp) revealed that the wild-type carp and its crosses had a much-improved survival over the crosses of the commercial lines themselves. These crosses set the starting point for breeding of commercial strains with improved resistance. Resistant fish had lower antibody titer against the virus suggesting that resistance might depend more on the innate immunity. A set of 500 microsateliite markers was developed and the markers are currently being used for generating a genetic linkage map for carp and for identifying disease resistance QTL. Fourteen candidate immune genes, some of which were duplicated, were cloned from the carp and SNP markers were identified in them. The expression of these genes varied between tissues and suggested functional divergence of some duplicated genes. Initial association between CyHV-3 resistance and one of the genes was found when SNP alleles in these genes were tested for their segregation between susceptible and resistant progeny. The results of this project have implications to the development of viral resistant commercial carp strains and effective immunization against this aggressive disease. The genetic and immunological knowledge accumulated in this project will not only promote carp and koi production but will also contribute to a broader understanding of fish immunogenetics.

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A Dense Genetic Linkage Map for Common Carp and Its Integration with a BAC-Based Physical Map

PLoS ONE ◽

10.1371/journal.pone.0063928 ◽

2013 ◽

Vol 8 (5) ◽

pp. e63928 ◽

Cited By ~ 30

Author(s):

Lan Zhao ◽

Yan Zhang ◽

Peifeng Ji ◽

Xiaofeng Zhang ◽

Zixia Zhao ◽

...

Keyword(s):

Linkage Map ◽

Common Carp ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Physical Map

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Development of a genetic linkage map for Pinus radiata and detection of pitch canker disease resistance associated QTLs

Trees ◽

10.1007/s00468-014-1090-2 ◽

2014 ◽

Vol 28 (6) ◽

pp. 1823-1835 ◽

Cited By ~ 10

Author(s):

P. Moraga-Suazo ◽

L. Orellana ◽

P. Quiroga ◽

C. Balocchi ◽

E. Sanfuentes ◽

...

Keyword(s):

Disease Resistance ◽

Linkage Map ◽

Pinus Radiata ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Pitch Canker ◽

Canker Disease

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An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

Scientific Reports ◽

10.1038/srep26693 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 50

Author(s):

Wenzhu Peng ◽

Jian Xu ◽

Yan Zhang ◽

Jianxin Feng ◽

Chuanju Dong ◽

...

Keyword(s):

High Resolution ◽

Linkage Map ◽

Common Carp ◽

Fine Mapping ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

High Density ◽

Sex Dimorphism ◽

Qtl Fine Mapping ◽

High Density Linkage Map

Abstract High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly.

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Screening of SSR markers associated with scale cover pattern and mapped to a genetic linkage map of common carp (Cyprinus carpio L.)

Journal of Applied Genetics ◽

10.1007/s13353-014-0250-9 ◽

2014 ◽

Vol 56 (2) ◽

pp. 261-269 ◽

Cited By ~ 1

Author(s):

Tongqian Xiao ◽

Cuiyun Lu ◽

Yulan Xu ◽

Chao Li ◽

Xianhu Zheng ◽

...

Keyword(s):

Linkage Map ◽

Ssr Markers ◽

Common Carp ◽

Cyprinus Carpio ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Common Carp Cyprinus Carpio ◽

Scale Cover ◽

Carp Cyprinus Carpio ◽

Cover Pattern

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Artemia sp. as a DNA vaccine vector for common carp Cyprinus carpio larvae

Jurnal Akuakultur Indonesia ◽

10.19027/jai.12.54-61 ◽

2014 ◽

Vol 12 (1) ◽

pp. 54

Author(s):

Sri Nuryati ◽

Sekar Sulistyaning Hadiwibowo ◽

. Alimuddin

Keyword(s):

Dna Vaccine ◽

Common Carp ◽

Cyprinus Carpio ◽

Herpes Virus ◽

Oral Vaccine ◽

Viral Disease ◽

Pcr Analysis ◽

Rt Pcr ◽

Glycoprotein Gene ◽

Herpès Virus

ABSTRACT Koi herpes virus (KHV) is one of the most common impetuses for disease on common carp Cyprinus carpio. Generally, viral disease is difficult to cure because virus is intra-cellular parasite, that virus survives, multiplies, and lives only if it on the host cell. Oral vaccine delivery through Artemia sp. is of one alternative way to overcome this problem. This experiment was carried out by analysis DNA vaccine expression encoding of glycoprotein gene (GP-11) on C. carpio. Bacteria containing plasmid Krt-GP-11 as vaccine is served through Artemia sp. as a vector. Artemia sp. was given for one and two times a week to three weeks old common carp. Organs of fish fed by Artemia sp. were analyzed every three days after vaccination. The expression of GP-11 in kidney in each treatment is also observed by the use of RT-PCR method, within ten days after vaccination. The experiment showed that dose of DNA vaccine in whole bacteria could be expressed is 106 cfu/mL in a once or twice provisions a week. DNA vaccine could be detected in three organs. RT-PCR analysis also showed that the expression of GP-11 can be detected in all tested organs. In conclusion, Artemia sp. can be used as a vector to carry plasmid GP-11 vaccine for common carp Cyprinus carpio larvae. Keywords: DNA vaccine, KHV, Artemia sp., common carp ABSTRAK Salah satu penyakit pada ikan mas (Cyprinus carpio) yang disebabkan oleh virus adalah koi herpes virus (KHV). Penyakit yang disebabkan oleh virus umumnya sulit untuk disembuhkan karena virus merupakan parasit intraseluler, yaitu virus hanya dapat hidup, bertahan hidup, dan memperbanyak diri di dalam sel inang. Metode pemberian vaksin DNA secara oral melalui Artemia sp. merupakan salah satu alternatif pengobatan yang diharapkan dapat menangani permasalahan penyakit pada ikan yang disebabkan oleh virus. Pada penelitian ini dilakukan uji ekspresi vaksin DNA yang menyandikan glikoprotein 11 (GP-11) pada ikan mas. Bakteri yang mengandung plasmid Krt-GP-11 sebagai vaksin diberikan melalui Artemia sp. sebagai pembawa vaksin. Pemberian Artemia sp. dilakukan satu dan dua kali seminggu pada ikan mas umur tiga minggu. Keberadaan DNA vaksin di usus, ginjal, dan insang dianalisis menggunakan metode PCR. Organ diambil setiap tiga hari setelah pemberian vaksin. Ekspresi gen GP-11 juga diamati pada organ ginjal di setiap perlakuan dengan menggunakan metode RT-PCR, pada sepuluh hari setelah pemberian vaksin. Hasil penelitian menunjukkan bahwa DNA vaksin yang diberikan dengan dosis 106 cfu/mL pada perlakuan satu dan dua kali seminggu dapat terdeteksi pada ketiga organ. Hasil RT-PCR menunjukkan bahwa ekspresi GP-11 dapat terdeteksi pada semua organ uji di setiap perlakuan. Dengan demikian Artemia sp. dapat digunakan sebagai vektor pembawa vaksin plasmid GP-11 dengan frekuensi pemberian vaksin untuk larva ikan mas. Kata kunci: vaksin DNA, KHV, Artemia sp., ikan mas

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High-Density GBS-Based Genetic Linkage Map Construction and QTL Identification Associated With Yellow Mosaic Disease Resistance in Bitter Gourd (Momordica charantia L.)

Frontiers in Plant Science ◽

10.3389/fpls.2021.671620 ◽

2021 ◽

Vol 12 ◽

Author(s):

Gurpreet Kaur ◽

Mamta Pathak ◽

Deepak Singla ◽

Abhishek Sharma ◽

Parveen Chhuneja ◽

...

Keyword(s):

Disease Resistance ◽

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Snp Markers ◽

Mosaic Disease ◽

Bitter Gourd ◽

Phenotypic Variance ◽

Spring Season ◽

Yellow Mosaic Disease

Yellow mosaic disease (YMD) in bitter gourd (Momordica charantia) is a devastating disease that seriously affects its yield. Although there is currently no effective method to control the disease, breeding of resistant varieties is the most effective and economic option. Moreover, quantitative trait locus (QTL) associated with resistance to YMD has not yet been reported. With the objective of mapping YMD resistance in bitter gourd, the susceptible parent “Punjab-14” and the resistant parent “PAUBG-6” were crossed to obtain F4 mapping population comprising 101 individuals. In the present study, the genotyping by sequencing (GBS) approach was used to develop the genetic linkage map. The map contained 3,144 single nucleotide polymorphism (SNP) markers, consisted of 15 linkage groups, and it spanned 2415.2 cM with an average marker distance of 0.7 cM. By adopting the artificial and field inoculation techniques, F4:5 individuals were phenotyped for disease resistance in Nethouse (2019), Rainy (2019), and Spring season (2020). The QTL analysis using the genetic map and phenotyping data identified three QTLs qYMD.pau_3.1, qYMD.pau_4.1, and qYMD.pau_5.1 on chromosome 3, 4, and 5 respectively. Among these, qYMD.pau_3.1, qYMD.pau_4.1 QTLs were identified during the rainy season, explaining the 13.5 and 21.6% phenotypic variance respectively, whereas, during the spring season, qYMD.pau_4.1 and qYMD.pau_5.1 QTLs were observed with 17.5 and 22.1% phenotypic variance respectively. Only one QTL qYMD.pau_5.1 was identified for disease resistance under nethouse conditions with 15.6% phenotypic variance. To our knowledge, this is the first report on the identification of QTLs associated with YMD resistance in bitter gourd using SNP markers. The information generated in this study is very useful in the future for fine-mapping and marker-assisted selection for disease resistance.

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A genetic linkage map and comparative genome analysis of common carp (Cyprinus carpio L.) using microsatellites and SNPs

Molecular Genetics and Genomics ◽

10.1007/s00438-011-0644-x ◽

2011 ◽

Vol 286 (3-4) ◽

Cited By ~ 36

Author(s):

Xianhu Zheng ◽

Youyi Kuang ◽

Xiaofeng Zhang ◽

Cuiyun Lu ◽

Dingchen Cao ◽

...

Keyword(s):

Linkage Map ◽

Common Carp ◽

Cyprinus Carpio ◽

Genome Analysis ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Comparative Genome Analysis ◽

Comparative Genome ◽

Common Carp Cyprinus Carpio ◽

Carp Cyprinus Carpio

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An EST-SSR based genetic linkage map and identification of QTLs for anthracnose disease resistance in water yam (Dioscorea alata L.)

PLoS ONE ◽

10.1371/journal.pone.0197717 ◽

2018 ◽

Vol 13 (10) ◽

pp. e0197717 ◽

Cited By ~ 5

Author(s):

Ranjana Bhattacharjee ◽

Christian O. Nwadili ◽

Christopher A. Saski ◽

Agre Paterne ◽

Brian E. Scheffler ◽

...

Keyword(s):

Disease Resistance ◽

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Dioscorea Alata ◽

Anthracnose Disease ◽

Water Yam

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A High-Density Genetic Linkage Map and Fine Mapping of QTL For Feed Conversion Efficiency in Common Carp (Cyprinus carpio)

Frontiers in Genetics ◽

10.3389/fgene.2021.778487 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xiaofeng Zhang ◽

Peixian Luan ◽

Dingchen Cao ◽

Guo Hu

Keyword(s):

High Resolution ◽

Linkage Map ◽

Common Carp ◽

Fine Mapping ◽

Cyprinus Carpio ◽

Feed Efficiency ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

High Density ◽

Feed Conversion

Feed conversion efficiency (FCE) is an economically crucial trait in fish, however, little progress has been made in genetics and genomics for this trait because phenotypes of the trait are difficult to measure. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,416 SNP markers for common carp (Cyprinus carpio) based on high throughput genotyping with the carp 250K single nucleotide polymorphism (SNP) array in a full-sib F1 family of mirror carp (Cyprinus carpio) consisting of 141 progenies. The linkage map contained 11,983 distinct loci and spanned 3,590.09 cM with an average locus interval of 0.33 cM. A total of 17 QTL for the FCE trait were detected on four LGs (LG9, LG20, LG28, and LG32), explaining 8.9–15.9% of the phenotypic variations. One major cluster containing eight QTL (qFCE1-28, qFCE2-28, qFCE3-28, qFCE4-28, qFCE5-28, qFCE6-28, qFCE7-28, and qFCE8-28) was detected on LG28. Two clusters consisting of four QTL (qFCE1-32, qFCE2-32, qFCE3-32, and qFCE4-32) and three QTL (qFCE1-20, qFCE2-20, and qFCE3-20) were detected on LG32 and LG20, respectively. Nine candidate genes (ACACA, SCAF4, SLC2A5, TNMD, PCDH1, FOXO, AGO1, FFAR3, and ARID1A) underlying the feed efficiency trait were also identified, the biological functions of which may be involved in lipid metabolism, carbohydrate metabolism, energy deposition, fat accumulation, digestion, growth regulation, and cell proliferation and differentiation according to GO (Gene Ontology). As an important tool, high-density and high-resolution genetic linkage maps play a crucial role in the QTL fine mapping of economically important traits. Our novel findings provided new insights that elucidate the genetic basis and molecular mechanism of feed efficiency and the subsequent marker-assisted selection breeding in common carp.

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