Articles

Landraces of snake melon, an ancient Middle Eastern crop, reveal extensive morphological and DNA diversity for potential genetic improvement

Snake melon (Cucumis melo var. flexuosus, “Faqqous”) is a traditional and ancient vegetable in the Mediterranean area. A collection of landraces from 42 grower fields in Israel and Palestinian territories was gro...

Authors: Samer Omari, Yuri Kamenir, Jennifer I. C. Benichou, Sarah Pariente, Hanan Sela and Rafael Perl-Treves

Genetic diversity of BoLA-DRB3 in South American Zebu cattle populations

Bovine leukocyte antigens (BoLAs) are used extensively as markers of disease and immunological traits in cattle. However, until now, characterization of BoLA gene polymorphisms in Zebu breeds using high resolu...

Authors: Shin-nosuke Takeshima, Claudia Corbi-Botto, Guillermo Giovambattista and Yoko Aida

TelNet - a database for human and yeast genes involved in telomere maintenance

The ends of linear chromosomes, the telomeres, comprise repetitive DNA sequences in complex with proteins that protects them from being processed by the DNA repair machinery. Cancer cells need to counteract th...

Authors: Delia M. Braun, Inn Chung, Nick Kepper, Katharina I. Deeg and Karsten Rippe

Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

Currently, genome-wide scans for positive selection signatures in commercial breed have been investigated. However, few studies have focused on selection footprints of indigenous breeds. Laiwu pig is an invalu...

Authors: Minhui Chen, Jiying Wang, Yanping Wang, Ying Wu, Jinluan Fu and Jian-feng Liu

RETRACTED ARTICLE: Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle

Genome-wide association studies (GWAS) have been successfully implemented in cattle research and breeding. However, moving from the associations to identifying the causal variants and revealing underlying mech...

Authors: Zexi Cai, Bernt Guldbrandtsen, Mogens Sandø Lund and Goutam Sahana

A deeper view into the significance of simple sequence repeats in pre-miRNAs provides clues for its possible roles in determining the function of microRNAs

The central tenet of ‘genome content’ has been that the ‘non-coding’ parts are highly enriched with ‘microsatellites’ or ‘Simple Sequence Repeats’ (SSRs). We presume that the presence and change in number of r...

Authors: Nisha Joy, Y. P. Maimoonath Beevi and E. V. Soniya

Hidden MHC genetic diversity in the Iberian ibex (Capra pyrenaica)

Defining hidden genetic diversity within species is of great significance when attempting to maintain the evolutionary potential of natural populations and conduct appropriate management. Our hypothesis is tha...

Authors: Samer Angelone, Michael J. Jowers, Anna Rita Molinar Min, Paulino Fandos, Paloma Prieto, Mario Pasquetti, Francisco Javier Cano-Manuel, Gregorio Mentaberre, Jorge Ramón López Olvera, Arián Ráez-Bravo, José Espinosa, Jesús M. Pérez, Ramón C. Soriguer, Luca Rossi and José Enrique Granados

Can metamorphosis survival during larval development in spiny lobster Sagmariasus verreauxi be improved through quantitative genetic inheritance?

One of the major impediments to spiny lobster aquaculture is the high cost of hatchery production due to the long and complex larval cycle and poor survival during the many moult stages, especially at metamorp...

Authors: Nguyen H. Nguyen, Quinn P. Fitzgibbon, Jane Quinn, Greg Smith, Stephen Battaglene and Wayne Knibb

Identification and characterization of karyotype in Passiflora hybrids using FISH and GISH

A great interest exists in the production of hybrid plants of the genus Passiflora given the beauty and exotic features of its flowers which have ornamental value. Hybrid paternity confirmation is therefore impor...

Authors: Gonçalo Santos Silva, Margarete Magalhães Souza, Cláusio Antônio Ferreira de Melo, Juan Domingo Urdampilleta and Eliana Regina Forni-Martins

Karyotype diversity and 2C DNA content in species of the Caesalpinia group

The Leguminosae family is the third-largest family of angiosperms, and Caesalpinioideae is its second-largest subfamily. A great number of species (approximately 205) are found in the Caesalpinia group within thi...

Authors: Polliana Silva Rodrigues, Margarete Magalhães Souza, Cláusio Antônio Ferreira Melo, Telma Nair Santana Pereira and Ronan Xavier Corrêa

Genetic loci for resistance to podocyte injury caused by the tensin2 gene deficiency in mice

Tensin2 is a focal adhesion-localized multidomain protein expressed in various tissues, and its dysfunction leads to alterations in podocytes. However, these podocyte-related manifestations are dependent on mu...

Authors: Yuki Takahashi, Hayato Sasaki, Shiori Okawara and Nobuya Sasaki

Genomic heritability estimates in sweet cherry reveal non-additive genetic variance is relevant for industry-prioritized traits

Sweet cherry is consumed widely across the world and provides substantial economic benefits in regions where it is grown. While cherry breeding has been conducted in the Pacific Northwest for over half a centu...

Authors: Julia Piaskowski, Craig Hardner, Lichun Cai, Yunyang Zhao, Amy Iezzoni and Cameron Peace

Power and precision of QTL mapping in simulated multiple porcine F2 crosses using whole-genome sequence information

During the last two decades, many QTL (quantitative trait locus) mapping experiments in pigs have been conducted using F2 crosses established from two outbred founder breeds. The founder breeds were frequently...

Authors: Markus Schmid, Robin Wellmann and Jörn Bennewitz

Genetic insights into dispersal distance and disperser fitness of African lions (Panthera leo) from the latitudinal extremes of the Kruger National Park, South Africa

Female lions generally do not disperse far beyond their natal range, while males can disperse distances of over 200 km. However, in bush-like ecosystems dispersal distances less than 25 km are reported. Here, ...

Authors: Pim van Hooft, Dewald F. Keet, Diana K. Brebner and Armanda D. S. Bastos

Including gene networks to predict calving difficulty in Holstein, Brown Swiss and Jersey cattle

Calving difficulty or dystocia has a great economic impact in the US dairy industry. Reported risk factors associated with calving difficulty are feto-pelvic disproportion, gestation length and conformation. D...

Authors: Francesco Tiezzi, Maria E. Arceo, John B. Cole and Christian Maltecca

RNA-seq analysis of lncRNA-controlled developmental gene expression during puberty in goat & rat

Puberty is a pivotal stage in female animal development, and marks the onset of reproductive capability. However, little is known about the function of lncRNAs (long noncoding RNAs) in puberty. Therefore, RNA-...

Authors: Xiaoxiao Gao, Jing Ye, Chen Yang, Lei Luo, Ya Liu, Jianping Ding, Yunhai Zhang, Yinghui Ling, Weiping Huang, Xiaorong Zhang, Kaifa Zhang, Xiumei Li, Jie Zhou, Fugui Fang and Zubing Cao

Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome-based markers

The tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. Continuous enrichment of public...

Authors: Offiong Ukpong Edet, June-Sik Kim, Masanori Okamoto, Kousuke Hanada, Tomoyuki Takeda, Masahiro Kishii, Yasir Serag Alnor Gorafi and Hisashi Tsujimoto

Refining a major QTL controlling spotted wilt disease resistance in cultivated peanut (Arachis hypogaea L.) and evaluating its contribution to the resistance variations in peanut germplasm

Spotted wilt, caused by tomato spotted wilt virus (TSWV), has been one of major diseases in cultivated peanut grown in the southeastern United States (US) since 1990. Previously a major quantitative trait locus (...

Authors: Zifan Zhao, Yu-Chien Tseng, Ze Peng, Yolanda Lopez, Charles Y. Chen, Barry L. Tillman, Phat Dang and Jianping Wang

A genome-wide association study identifies candidate loci associated to syringomyelia secondary to Chiari-like malformation in Cavalier King Charles Spaniels

Syringomyelia (SM) is a common condition affecting brachycephalic toy breed dogs and is characterized by the development of fluid-filled cavities within the spinal cord. It is often concurrent with a complex d...

Authors: Frédéric Ancot, Philippe Lemay, Susan P. Knowler, Karen Kennedy, Sandra Griffiths, Giunio Bruto Cherubini, Jane Sykes, Paul J. J. Mandigers, Guy A. Rouleau, Clare Rusbridge and Zoha Kibar

Common variants in the hERG (KCNH2) voltage-gated potassium channel are associated with altered fasting and glucose-stimulated plasma incretin and glucagon responses

Patients with long QT syndrome due to rare loss-of-function mutations in the human ether-á-go-go-related gene (hERG) have prolonged QT interval, risk of arrhythmias, increased secretion of insulin and incretins a...

Authors: Line Engelbrechtsen, Yuvaraj Mahendran, Anna Jonsson, Anette Prior Gjesing, Peter E. Weeke, Marit E. Jørgensen, Kristine Færch, Daniel R. Witte, Jens J. Holst, Torben Jørgensen, Niels Grarup, Oluf Pedersen, Henrik Vestergaard, Signe Torekov, Jørgen K. Kanters and Torben Hansen

Whole-genome scan reveals significant non-additive effects for sire conception rate in Holstein cattle

Service sire has a considerable impact on reproductive success in dairy cattle. Most gene mapping studies for bull fertility have focused on additive effects, while non-additive effects have been largely ignor...

Authors: Paula Nicolini, Rocío Amorín, Yi Han and Francisco Peñagaricano

Correction to: High density marker panels, SNPs prioritizing and accuracy of genomic selection

The original version of this article [1], published on 5 January 2018, contained 3 formatting errors. In this Correction the affected parts of the article are shown. The original article has been updated.

Authors: Ling-Yun Chang, Sajjad Toghiani, Ashley Ling, Sammy E. Aggrey and Romdhane Rekaya

Genetic diversity and ex situ conservation of Loropetalum subcordatum, an endangered species endemic to China

Loropetalum subcordatum is an endangered species endemic to China that is characterized by narrow distribution, small population size, and delayed fertilization. However, the genetic diversity of the entire extan...

Authors: Bai-Jun Li, Jie-Yu Wang, Zhong-Jian Liu, Xue-Ying Zhuang and Jiu-Xiang Huang

Diversity of plant defense elicitor peptides within the Rosaceae

Plant elicitor peptides (Peps) are endogenous molecules that induce and amplify the first line of inducible plant defense, known as pattern-triggered immunity, contributing to protect plants against attack by ...

Authors: Cristina Ruiz, Anna Nadal, Laura Foix, Laura Montesinos, Emilio Montesinos and Maria Pla

DArT, SNP, and SSR analyses of genetic diversity in Lolium perenne L. using bulk sampling

Lolium perenne L. is the most important forage grass species in temperate regions. It is also considered as a sustainable source of biomass for energy production. However, improvement in biomass yield has been li...

Authors: Siyang Liu, Ulf Feuerstein, Wilbert Luesink, Sabine Schulze, Torben Asp, Bruno Studer, Heiko C. Becker and Klaus J. Dehmer

Detecting TF-miRNA-gene network based modules for 5hmC and 5mC brain samples: a intra- and inter-species case-study between human and rhesus

Study of epigenetics is currently a high-impact research topic. Multi stage methylation is also an area of high-dimensional prospect. In this article, we provide a new study (intra and inter-species study) on ...

Authors: Ujjwal Maulik, Sagnik Sen, Saurav Mallik and Sanghamitra Bandyopadhyay

Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivars

Diversity in crops is fundamental for plant breeding efforts. An accurate assessment of genetic diversity, using molecular markers, such as single nucleotide polymorphism (SNP), must be able to reveal the stru...

Authors: Martin E. Tagliotti, Sofia I. Deperi, Maria C. Bedogni, Ruofang Zhang, Norma C. Manrique Carpintero, Joseph Coombs, David Douches and Marcelo A. Huarte

Rare variant association analysis in case-parents studies by allowing for missing parental genotypes

The development of next-generation sequencing technologies has facilitated the identification of rare variants. Family-based design is commonly used to effectively control for population admixture and substruc...

Authors: Yumei Li, Yang Xiang, Chao Xu, Hui Shen and Hongwen Deng

Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton

Late embryogenesis abundant (LEA) proteins are large groups of hydrophilic proteins with major role in drought and other abiotic stresses tolerance in plants. In-depth study and characterization of LEA protein...

Authors: Richard Odongo Magwanga, Pu Lu, Joy Nyangasi Kirungu, Hejun Lu, Xingxing Wang, Xiaoyan Cai, Zhongli Zhou, Zhenmei Zhang, Haron Salih, Kunbo Wang and Fang Liu

Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice

Balancing panicle-related traits such as panicle length and the numbers of primary and secondary branches per panicle, is key to improving the number of spikelets per panicle in rice. Identifying genetic infor...

Authors: Su Jang, Yunjoo Lee, Gileung Lee, Jeonghwan Seo, Dongryung Lee, Yoye Yu, Joong Hyoun Chin and Hee-Jong Koh

High density marker panels, SNPs prioritizing and accuracy of genomic selection

The availability of high-density (HD) marker panels, genome wide variants and sequence data creates an unprecedented opportunity to dissect the genetic basis of complex traits, enhance genomic selection (GS) a...

Authors: Ling-Yun Chang, Sajjad Toghiani, Ashley Ling, Sammy E. Aggrey and Romdhane Rekaya

De novo transcriptome sequencing and analysis of male and female swimming crab (Portunus trituberculatus) reproductive systems during mating embrace (stage II)

The swimming crab Portunus trituberculatus is one of the most commonly farmed crustaceans in China. As one of the most widely known and high-value edible crabs, it crab supports large crab fishery and aquaculture...

Authors: Zhengfei Wang, Linxia Sun, Weibing Guan, Chunlin Zhou, Boping Tang, Yongxu Cheng, Jintian Huang and Fujun Xuan

Genome-wide association study of seedling stage salinity tolerance in temperate japonica rice germplasm

Salinity has a significant impact on rice production in coastal, arid and semi-arid areas in many countries, including countries growing temperate rice, such as Kazakhstan. Recently, the complete genomes of 30...

Authors: Dariga Batayeva, Benedick Labaco, Changrong Ye, Xiaolin Li, Bakdaulet Usenbekov, Aiman Rysbekova, Gulzhamal Dyuskalieva, Georgina Vergara, Russell Reinke and Hei Leung

High resolution melting curve analysis targeting the HBB gene mutational hot-spot offers a reliable screening approach for all common as well as most of the rare beta-globin gene mutations in Bangladesh

Bangladesh lies in the global thalassemia belt, which has a defined mutational hot-spot in the beta-globin gene. The high carrier frequencies of beta-thalassemia trait and hemoglobin E-trait in Bangladesh nece...

Authors: Md Tarikul Islam, Suprovath Kumar Sarkar, Nusrat Sultana, Mst. Noorjahan Begum, Golam Sarower Bhuyan, Shezote Talukder, A. K. M. Muraduzzaman, Md Alauddin, Mohammad Sazzadul Islam, Pritha Promita Biswas, Aparna Biswas, Syeda Kashfi Qadri, Tahmina Shirin, Bilquis Banu, Salma Sadya, Manzoor Hussain…

Upregulation of NETO2 gene in colorectal cancer

Neuropilin and tolloid-like 2 (NETO2) is a single-pass transmembrane protein that has been shown primarily implicated in neuron-specific processes. Upregulation of NETO2 gene was also detected in several cancer t...

Authors: Maria S. Fedorova, Anastasiya V. Snezhkina, Elena A. Pudova, Ivan S. Abramov, Anastasiya V. Lipatova, Sergey L. Kharitonov, Asiya F. Sadritdinova, Kirill M. Nyushko, Kseniya M. Klimina, Mikhail M. Belyakov, Elena N. Slavnova, Nataliya V. Melnikova, Maria A. Chernichenko, Dmitry V. Sidorov, Marina V. Kiseleva, Andrey D. Kaprin…

Genetics at Belyaev Conference – 2017: introductory note

Authors: Yuriy L. Orlov, Ancha V. Baranova, Tatiana V. Tatarinova and Nikolay A. Kolchanov

Generation of megabase-scale deletions, inversions and duplications involving the Contactin-6 gene in mice by CRISPR/Cas9 technology

Copy Number Variation (CNV) of the human CNTN6 gene (encoding the contactin-6 protein), caused by deletions or duplications, is responsible for severe neurodevelopmental impairments, often in combination with fac...

Authors: Alexei N. Korablev, Irina A. Serova and Oleg L. Serov

A compendium and functional characterization of mammalian genes involved in adaptation to Arctic or Antarctic environments

Many mammals are well adapted to surviving in extremely cold environments. These species have likely accumulated genetic changes that help them efficiently cope with low temperatures. It is not known whether t...

Authors: Nikolay S. Yudin, Denis M. Larkin and Elena V. Ignatieva

Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe

The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves of Turkic and Uralic-...

Authors: Petr Triska, Nikolay Chekanov, Vadim Stepanov, Elza K. Khusnutdinova, Ganesh Prasad Arun Kumar, Vita Akhmetova, Konstantin Babalyan, Eugenia Boulygina, Vladimir Kharkov, Marina Gubina, Irina Khidiyatova, Irina Khitrinskaya, Ekaterina E. Khrameeva, Rita Khusainova, Natalia Konovalova, Sergey Litvinov…

Application of geographic population structure (GPS) algorithm for biogeographical analyses of populations with complex ancestries: a case study of South Asians from 1000 genomes project

The utilization of biological data to infer the geographic origins of human populations has been a long standing quest for biologists and anthropologists. Several biogeographical analysis tools have been devel...

Authors: Ranajit Das and Priyanka Upadhyai

DEP1 gene in wheat species with normal, compactoid and compact spikes

In rice, a variant of DEP1 gene results in erect panicle architecture, well-developed vascular bundles, an increase in the number of grains per panicle and a consequent increase in the grain yield. Interestingly,...

Authors: Valeriya Vavilova, Irina Konopatskaia, Anastasia E. Kuznetsova, Alexandr Blinov and Nikolay P. Goncharov

Novel methods for genotype imputation to whole-genome sequence and a simple linear model to predict imputation accuracy

Accurate imputation plays a major role in genomic studies of livestock industries, where the number of genotyped or sequenced animals is limited by costs. This study explored methods to create an ideal referen...

Authors: Steven G. Larmer, Mehdi Sargolzaei, Luiz F. Brito, Ricardo V. Ventura and Flávio S. Schenkel

An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench)

Drought is the most disastrous abiotic stress that severely affects agricultural productivity worldwide. Understanding the biological basis of drought-regulated traits, requires identification and an in-depth ...

Authors: Adugna Abdi Woldesemayat, Peter Van Heusden, Bongani K. Ndimba and Alan Christoffels

Evolutionary history of the NAM-B1 gene in wild and domesticated tetraploid wheat

The NAM-B1 gene in wheat has for almost three decades been extensively studied and utilized in breeding programs because of its significant impact on grain protein and mineral content and pleiotropic effects on s...

Authors: Maria Lundström, Matti W. Leino and Jenny Hagenblad

Comparison of weighting approaches for genetic risk scores in gene-environment interaction studies

Weighted genetic risk scores (GRS), defined as weighted sums of risk alleles of single nucleotide polymorphisms (SNPs), are statistically powerful for detection gene-environment (GxE) interactions. To assign w...

Authors: Anke Hüls, Ursula Krämer, Christopher Carlsten, Tamara Schikowski, Katja Ickstadt and Holger Schwender

Investigating population continuity with ancient DNA under a spatially explicit simulation framework

Recent advances in sequencing technologies have allowed for the retrieval of ancient DNA data (aDNA) from skeletal remains, providing direct genetic snapshots from diverse periods of human prehistory. Comparin...

Authors: Nuno Miguel Silva, Jeremy Rio and Mathias Currat

Correction to: Mapping of leptin and its syntenic genes to chicken chromosome 1p

After the publication of this work [1] an error was noticed in one of the author surnames. The author name Leif Anderson should be spelt as Leif Andersson.

Authors: Eyal Seroussi, Frédérique Pitel, Sophie Leroux, Mireille Morisson, Susanne Bornelöv, Shoval Miyara, Sara Yosefi, Larry A. Cogburn, David W. Burt, Leif Andersson and Miriam Friedman-Einat

Functional polymorphisms in asporin and CILP together with joint loading predispose to hand osteoarthritis

Osteoarthritis (OA) is the most common degenerative joint disease afflicting people in the Western world and has a strong genetic influence. The aim of this study was to examine the association of two known fu...

Authors: Mari Taipale, Svetlana Solovieva, Päivi Leino-Arjas and Minna Männikkö

Evaluation of methods and marker Systems in Genomic Selection of oil palm (Elaeis guineensis Jacq.)

Genomic selection (GS) uses genome-wide markers as an attempt to accelerate genetic gain in breeding programs of both animals and plants. This approach is particularly useful for perennial crops such as oil pa...

Authors: Qi Bin Kwong, Chee Keng Teh, Ai Ling Ong, Fook Tim Chew, Sean Mayes, Harikrishna Kulaveerasingam, Martti Tammi, Suat Hui Yeoh, David Ross Appleton and Jennifer Ann Harikrishna

Genome-wide association study of coronary artery calcified atherosclerotic plaque in African Americans with type 2 diabetes

Coronary artery calcified atherosclerotic plaque (CAC) predicts cardiovascular disease (CVD). Despite exposure to more severe conventional CVD risk factors, African Americans (AAs) are less likely to develop C...

Authors: Jasmin Divers, Nicholette D. Palmer, Carl D. Langefeld, W. Mark Brown, Lingyi Lu, Pamela J. Hicks, S. Carrie Smith, Jianzhao Xu, James G. Terry, Thomas C. Register, Lynne E. Wagenknecht, John S. Parks, Lijun Ma, Gary C. Chan, Sarah G. Buxbaum, Adolfo Correa…