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Marker assisted selection

Richard G Tait, Robert A Cushman, Anthony K McNeel, Eduardo Casas, Timothy P L Smith, Harvey C Freetly, Gary L Bennett
Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. An Angus population was subjected to marker assisted selection for multiple years to equalize CAPN1 haplotypes, CAST, and GHR genetic marker frequencies. The objective was to estimate the pleiotropic effects of these carcass quality oriented markers for body weight, reproduction, and first calf performance traits in 174 replacement beef females which were managed under 2 post-weaning development protocols...
February 3, 2018: Theriogenology
Zhenliang Chen, Yunqiu Yao, Peipei Ma, Qishan Wang, Yuchun Pan
Since milk yield is a highly important economic trait in dairy cattle, the genome-wide association study (GWAS) is vital to explain the genetic architecture underlying milk yield and to perform marker-assisted selection (MAS). In this study, we adopted a haplotype-based empirical Bayesian GWAS to identify the loci and candidate genes for milk yield. A total of 1 092 Holstein cows were sequenced by using the genotyping by genome reducing and sequencing (GGRS) method. After filtering, 164 312 high-confidence SNPs and 13 476 haplotype blocks were identified to use for GWAS...
2018: PloS One
Albert G Remacle, Jennifer Dolkas, Mila Angert, Swathi K Hullugundi, Andrei V Chernov, R Carter W Jones, Veronica I Shubayev, Alex Y Strongin
Sciatic nerve chronic constriction injury (CCI) in rodents produces nerve demyelination via proteolysis of myelin basic protein (MBP), the major component of myelin sheath. Proteolysis releases the cryptic MBP epitope, a demyelination marker, which is hidden in the native MBP fold. It has never been established if the proteolytic release of this cryptic MBP autoantigen stimulates the post-injury increase in the respective circulating autoantibodies. To measure these autoantibodies, we developed the ELISA that employed the cryptic 84-104 MBP sequence (MBP84-104) as bait...
February 8, 2018: Journal of Immunological Methods
M Teissier, M P Sanchez, M Boussaha, A Barbat, C Hoze, C Robert-Granie, P Croiseau
As a result of the 1000 Bull Genome Project, it has become possible to impute millions of variants, with many of these potentially causative for traits of interest, for thousands of animals that have been genotyped with medium-density chips. This enormous source of data opens up very interesting possibilities for the inclusion of these variants in genomic evaluations. However, for computational reasons, it is not possible to include all variants in genomic evaluation procedures. One potential approach could be to select the most relevant variants based on the results of genome-wide association studies (GWAS); however, the identification of causative mutations is still difficult with this method, partly because of weak imputation accuracy for rare variants...
February 7, 2018: Journal of Dairy Science
Xiaoyun Jia, Hantao Wang, Chaoyou Pang, Qifeng Ma, Junji Su, Hengling Wei, Meizhen Song, Shuli Fan, Shuxun Yu
Gossypium hirsutum L. is the most important fiber crop worldwide and contributes to more than 95% of global cotton production. Marker-assisted selection (MAS) is an effective approach for improving fiber quality, and quantitative trait loci (QTL) mapping of fiber quality traits is important for cotton breeding. In this study, a permanent intra-specific recombinant inbred line (RIL) population containing 137 families was used for fiber quality testing. Based on a previously reported high-density genetic map with an average marker distance of 0...
February 8, 2018: Molecular Genetics and Genomics: MGG
B Drinkwater, B K Clarke, J Jones, J Ratcliffe, P Deel-Smith, S C Cooper
BACKGROUND AND AIMS: Home parenteral nutrition (HPN) for palliation has little evidence supporting existing guidance. Patient selection remains challenging. We aimed to evaluate use of palliative HPN in our service against ESPEN guidance, and to identify potential prognostic indicators. METHODS: Palliative care patients commenced on HPN were identified. Medical notes, computer records and HPN database were accessed to identify patient demographics, primary diagnosis and aetiology of intestinal failure, blood test results potentially associated with prognosis (eGFR, albumin, CRP, Hb), presence of ascites, and PN duration...
December 2017: Clinical Nutrition ESPEN
Kaori Ando, Sheri Rynearson, Kebede T Muleta, Jhonatan Gedamu, Bedada Girma, Nilsa A Bosque-Pérez, Ming-Shun Chen, Mike O Pumphrey
Northern areas of the western United States are one of the most productive wheat growing regions in the United States. Increasing productivity through breeding is hindered by several biotic stresses which slow and constrain targeted yield improvement. In order to understand genetic variation for stripe rust (Puccinia striiformis f. sp. tritici), Septoria tritici blotch (Mycosphaerella graminicola), and Hessian fly (Mayetiola destructor) in regional germplasm, a panel of 408 elite spring wheat lines was characterized and genotyped with an Illumina 9K wheat single nucleotide polymorphism (SNP) chip to enable genome-wide association study (GWAS) analyses...
2018: PloS One
Yang Cui, Yanghai Zhang, Zhenyu Wei, Jiayang Gao, Ting Yu, Rui Chen, Xiaoyan Lv, Chuanying Pan
Lysine specific demethylase 5B gene (KDM5B, also known as JARID1B or PLU-1), encoding an enzyme of the lysine-specific histone demethylase family, has been reported to regulate androgen receptor transcriptional activity and male reproduction. To fully study the expression characteristics and genetic effects of pig KDM5B gene, the objective of this study was to investigate the mRNA expression profiles of KDM5B among different tissues and testicular cells (spermatogonia stem cells, SSCs; sertoli cells, SCs; leydig cells, LCs), as well as to explore the insertion/deletion (indel) variations of this gene...
January 30, 2018: Gene
Raquel B Ariede, Milena V Freitas, Milene E Hata, Vito A Mastrochirico-Filho, Fabiana Pilarski, Sergio R Batlouni, Fábio Porto-Foresti, Diogo T Hashimoto
Tambaqui, Colossoma macropomum, is the main native fish species produced in Brazil, and is an important species for genetic improvement in aquaculture. In addition, breeding studies on this species can be optimized with the use of molecular markers associated with productive phenotypes. The objective of the present study was to test the performance of growth traits and resistance to the bacteria, Aeromonas hydrophila, in association with microsatellite markers in C. macropomum. In this study, three full-sib families were subjected to bacterial challenge and morphometric growth assessments...
2018: Frontiers in Genetics
XiaoLei Shi, Long Yan, ChunYan Yang, WeiWen Yan, David Octor Moseley, Tao Wang, BingQiang Liu, Rui Di, PengYin Chen, MengChen Zhang
BACKGROUND: Identification of the quantitative trait locus (QTL) underlying salt tolerance is a prerequisite for marker-assisted selection in the salt-tolerant breeding process. METHODS: In this study, the recombinant inbred lines derived from the salt-tolerant elite soybean cultivar 'Jidou 12' and the salt-sensitive elite cultivar 'Ji NF 58' were used to identify the QTL associated with salt tolerance, using both salt tolerance rating (STR) and leaf chlorophyll content (SPAD) as indicators...
February 5, 2018: BMC Research Notes
Kengo Matsumoto, Yuya Ota, Satomi Seta, Yukinori Nakayama, Teppei Ohno, Ritsuko Mizobuchi, Hiroyuki Sato
Rice brown spot (BS), caused by Bipolaris oryzae, is one of the major diseases of rice in Japan. Quantitative resistance has been observed in local cultivars (e.g., CH45), but no economically useful resistant variety has been bred. Using simple sequence repeat (SSR) polymorphic markers, we conducted quantitative trait locus (QTL) analysis of BS resistance in backcross inbred lines (BILs) from a cross between indica CH45 (resistant) and japonica Koshihikari (susceptible). On the basis of field disease evaluations in 2015 and 2016, four QTLs contributing to BS resistance were identified on chromosomes 2 (qBSR2-kc), 7 (qBSR7-kc), 9 (qBSR9-kc), and 11 (qBSR11-kc)...
December 2017: Breeding Science
Yongbin Qi, Linyou Wang, Junmei Gui, Lixia Zhang, Qinglong Liu, Jianjun Wang
The fertility conversion of photoperiod thermo-sensitive genic male sterility (P/TGMS) lines in rice is mostly regulated by the P/TGMS genes in different environmental conditions. A point mutation with G-C on the pms3 (p/tms12-1) gene regulates the pollen fertility of Nongken58S and a large amount of Nongken58S-derived lines. In this study, we developed and designed a functional co-dominant marker according to the SNP loci for the pms3 (p/tms12-1) gene. We can differentiate the SNP loci in pms3 (p/tms12-1) gene from another TGMS lines and inbred cultivars using the dpms3-54 marker...
December 2017: Breeding Science
Sudhakar Pandey, Waquar Akhter Ansari, Maneesh Pandey, Bijendra Singh
In the present study, genetic variation among 40 cucumber genotypes was analyzed by means of morpho-physiological traits and 21 EST-SSR markers. Diversity was observed for morpho-physiological characters like days to 50% female flowering (37-46.9, number of fruits/plant (1.33-5.80), average fruit weight (41-333), vine length (36-364), relative water content (58.5-92.7), electrolyte leakage (15.9-37.1), photosynthetic efficiency (0.40-0.75) and chlorophyll concentration index (11.1-28.6). The pair wise Jaccard similarity coefficient ranged from 0...
February 2018: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
Naeela Qureshi, Harbans Bariana, Vikas Venu Kumran, Sivasamy Muruga, Kerrie L Forrest, Mathew J Hayden, Urmil Bansal
A new leaf rust resistance gene Lr79 has been mapped in the long arm of chromosome 3B and a linked marker was identified for marker-assisted selection. Aus26582, a durum wheat landrace from the A. E. Watkins Collection, showed seedling resistance against durum-specific and common wheat-specific Puccinia triticina (Pt) pathotypes. Genetic analysis using a recombinant inbred line (RIL) population developed from a cross between Aus26582 and the susceptible parent Bansi with Australian Pt pathotype showed digenic inheritance and the underlying loci were temporarily named LrAW2 and LrAW3...
February 2, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Miaomiao Zhang, Changpin Zhou, Zhijiao Song, Qijie Weng, Mei Li, Hongxia Ji, Xiaoyong Mo, Huanhua Huang, Wanhong Lu, Jianzhong Luo, Fagen Li, Siming Gan
Genomic loci related with resistance to gall-inducing insects have not been identified in any plants. Here, association mapping was used to identify molecular markers for resistance to the gall wasp Leptocybe invasa in two Eucalyptus species. A total of 86 simple sequence repeats (SSR) markers were screened out from 839 SSRs and used for association mapping in E. grandis. By applying the mixed linear model, seven markers were identified to be associated significantly (P ≤ 0.05) with the gall wasp resistance in E...
February 2, 2018: Scientific Reports
C N Neeraja, Kalyani S Kulkarni, P Madhu Babu, D Sanjeeva Rao, K Surekha, V Ravindra Babu
Polished rice is poor source of micronutrients, however wide genotypic variability exists for zinc uptake and remobilization and zinc content in brown and polished grains in rice. Two landraces (Chittimutyalu and Kala Jeera Joha) and one popular improved variety (BPT 5204) were grown under zinc sufficient soil and their analyses showed high zinc in straw of improved variety, but high zinc in polished rice in landraces suggesting better translocation ability of zinc into the grain in landraces. Transcriptome analyses of the panicle tissue showed 41182 novel transcripts across three samples...
2018: PloS One
Jie Li, Sarantsetseg Erdenee, Shaoli Zhang, Zhenyu Wei, Meng Zhang, Yunyun Jin, Hui Wu, Hong Chen, Xiuzhu Sun, Hongwei Xu, Yong Cai, Xianyong Lan
Prion protein (PRNP) gene is well known for affecting mammal transmissible spongiform encephalopathies (TSE), and is also reported to regulate phenotypic traits (e.g. growth traits) in healthy ruminants. To identify the insertion/deletion (indel) variations of the PRNP gene and evaluate their effects on growth traits, 768 healthy individuals from five sheep breeds located in China and Mongolia were identified and analyzed. Herein, four novel indel polymorphisms, namely, Intron-1-insertion-7bp (I1-7bp), Intron-2-insertion-15bp (I2-15bp), Intron-2-insertion-19bp (I2-19bp), and 3' UTR-insertion-7bp (3' UTR-7bp), were found in the sheep PRNP gene...
February 2, 2018: Prion
Aolin Jia, Yan Ren, Fengmei Gao, Guihong Yin, Jindong Liu, Lu Guo, Jizhou Zheng, Zhonghu He, Xianchun Xia
Four QTLs for adult-plant resistance to powdery mildew were mapped in the Zhou8425B/Chinese Spring population, and a new QTL on chromosome 3B was validated in 103 wheat cultivars derived from Zhou8425B. Zhou8425B is an elite wheat (Triticum aestivum L.) line widely used as a parent in Chinese wheat breeding programs. Identification of genes for adult-plant resistance (APR) to powdery mildew in Zhou8425B is of high importance for continued controlling the disease. In the current study, the high-density Illumina iSelect 90K single-nucleotide polymorphism (SNP) array was used to map quantitative trait loci (QTL) for APR to powdery mildew in 244 recombinant inbred lines derived from the cross Zhou8425B/Chinese Spring...
February 1, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Ovidiu Chioncel, Sean P Collins, Stephen J Greene, Peter S Pang, Andrew P Ambrosy, Elena-Laura Antohi, Muthiah Vaduganathan, Javed Butler, Mihai Gheorghiade
Acute Heart Failure (AHF) is a " multi-event disease" and hospitalisation is a critical event in the clinical course of HF. Despite relatively rapid relief of symptoms, hospitalisation for AHF is followed by an increased risk of death and re-hospitalisation. In AHF, risk stratification from clinically available data is increasingly important in evaluating long-term prognosis. From the perspective of patients, information on the risk of mortality and re-hospitalisation would be helpful in providing patients with insight into their disease...
November 2017: Cardiac Failure Review
Ayaka Nakajima, Fuki Kawaguchi, Yoshinobu Uemoto, Moriyuki Fukushima, Emi Yoshida, Eiji Iwamoto, Takayuki Akiyama, Namiko Kohama, Eiji Kobayashi, Takeshi Honda, Kenji Oyama, Hideyuki Mannen, Shinji Sasazaki
The objective of this study was to identify genomic regions associated with fat-related traits using a Japanese Black cattle population in Hyogo. From 1836 animals, those with high or low values were selected on the basis of corrected phenotype and then pooled into high and low groups (n = 100 each), respectively. DNA pool-based genome-wide association study (GWAS) was performed using Illumina BovineSNP50 BeadChip v2 with three replicate assays for each pooled sample. GWAS detected that two single nucleotide polymorphisms (SNPs) on BTA7 (ARS-BFGL-NGS-35463 and Hapmap23838-BTA-163815) and one SNP on BTA12 (ARS-BFGL-NGS-2915) significantly affected fat percentage (FAR)...
January 30, 2018: Animal Science Journal, Nihon Chikusan Gakkaihō
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