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Marker assisted selection

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https://www.readbyqxmd.com/read/28228768/genome-wide-single-nucleotide-polymorphisms-in-cms-and-restorer-lines-discovered-by-genotyping-using-sequencing-and-association-with-marker-combining-ability-for-12-yield-related-traits-in-oryza-sativa-l-subsp-japonica
#1
Imdad U Zaid, Weijie Tang, Erbao Liu, Sana U Khan, Hui Wang, Edzesi W Mawuli, Delin Hong
Heterosis or hybrid vigor is closely related with general combing ability (GCA) of parents and special combining ability (SCA) of combinations. The evaluation of GCA and SCA facilitate selection of parents and combinations in heterosis breeding. In order to improve combining ability (CA) by molecular marker assist selection, it is necessary to identify marker loci associated with the CA. To identify the single nucleotide polymorphisms (SNP) loci associated with CA in the parental genomes of japonica rice, genome-wide discovered SNP loci were tested for association with the CA of 18 parents for 12 yield-related traits...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28222201/linkage-and-mapping-of-quantitative-trait-loci-associated-with-angular-leaf-spot-and-powdery-mildew-resistance-in-common-beans
#2
Denis Bassi, Boris Briñez, Juliana Santa Rosa, Paula Rodrigues Oblessuc, Caléo Panhoca de Almeida, Stella Maris Nucci, Larissa Chariel Domingos da Silva, Alisson Fernando Chiorato, Rosana Pereira Vianello, Luis Eduardo Aranha Camargo, Matthew Wohlgemuth Blair, Luciana Lasry Benchimol-Reis
Angular leaf spot (ALS) and powdery mildew (PWM) are two important fungi diseases causing significant yield losses in common beans. In this study, a new genetic linkage map was constructed using single sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), in a segregating population derived from the AND 277 x SEA 5 cross, with 105 recombinant inbred lines. Phenotypic evaluations were performed in the greenhouse to identify quantitative trait loci (QTLs) associated with resistance by means of the composite interval mapping analysis...
February 20, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28220132/identification-of-marker-trait-associations-for-lint-traits-in-cotton
#3
Muhammad A Iqbal, Mehboob-Ur- Rahman
Harvesting high quality lint, a long-awaited breeding goal-accomplished partly, can be achieved by identifying DNA markers which could be used for diagnosing cotton plants containing the desired traits. In the present studies, a total of 185 cotton genotypes exhibiting diversity for lint traits were selected from a set of 546 genotypes evaluated for fiber traits in 2009. These genotypes were extensively studied for three consecutive years (2011-2013) at three different locations. Significant genetic variations were found for average boll weight, ginning out turn (GOT), micronaire value, staple length, fiber bundle strength, and uniformity index...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28219347/aquaculture-genomics-genetics-and-breeding-in-the-united-states-current-status-challenges-and-priorities-for-future-research
#4
EDITORIAL
Hisham Abdelrahman, Mohamed ElHady, Acacia Alcivar-Warren, Standish Allen, Rafet Al-Tobasei, Lisui Bao, Ben Beck, Harvey Blackburn, Brian Bosworth, John Buchanan, Jesse Chappell, William Daniels, Sheng Dong, Rex Dunham, Evan Durland, Ahmed Elaswad, Marta Gomez-Chiarri, Kamal Gosh, Ximing Guo, Perry Hackett, Terry Hanson, Dennis Hedgecock, Tiffany Howard, Leigh Holland, Molly Jackson, Yulin Jin, Karim Kahlil, Thomas Kocher, Tim Leeds, Ning Li, Lauren Lindsey, Shikai Liu, Zhanjiang Liu, Kyle Martin, Romi Novriadi, Ramjie Odin, Yniv Palti, Eric Peatman, Dina Proestou, Guyu Qin, Benjamin Reading, Caird Rexroad, Steven Roberts, Mohamed Salem, Andrew Severin, Huitong Shi, Craig Shoemaker, Sheila Stiles, Suxu Tan, Kathy F J Tang, Wilawan Thongda, Terrence Tiersch, Joseph Tomasso, Wendy Tri Prabowo, Roger Vallejo, Hein van der Steen, Khoi Vo, Geoff Waldbieser, Hanping Wang, Xiaozhu Wang, Jianhai Xiang, Yujia Yang, Roger Yant, Zihao Yuan, Qifan Zeng, Tao Zhou
Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28219341/integrating-genetic-maps-in-bambara-groundnut-vigna-subterranea-l-verdc-and-their-syntenic-relationships-among-closely-related-legumes
#5
Wai Kuan Ho, Hui Hui Chai, Presidor Kendabie, Nariman Salih Ahmad, Jaeyres Jani, Festo Massawe, Andrzej Kilian, Sean Mayes
BACKGROUND: Bambara groundnut [Vigna subterranea (L) Verdc.] is an indigenous legume crop grown mainly in subsistence and small-scale agriculture in sub-Saharan Africa for its nutritious seeds and its tolerance to drought and poor soils. Given that the lack of ex ante sequence is often a bottleneck in marker-assisted crop breeding for minor and underutilised crops, we demonstrate the use of limited genetic information and resources developed within species, but linked to the well characterised common bean (Phaseolus vulgaris) genome sequence and the partially annotated closely related species; adzuki bean (Vigna angularis) and mung bean (Vigna radiata)...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28216998/genetic-mapping-of-yield-traits-using-ril-population-derived-from-fuchuan-dahuasheng-and-icg6375-of-peanut-arachis-hypogaea-l
#6
Yuning Chen, Xiaoping Ren, Yanli Zheng, Xiaojing Zhou, Li Huang, Liying Yan, Yongqing Jiao, Weigang Chen, Shunmou Huang, Liyun Wan, Yong Lei, Boshou Liao, Dongxin Huai, Wenhui Wei, Huifang Jiang
The genetic architecture determinants of yield traits in peanut (Arachis hypogaea L.) are poorly understood. In the present study, an effort was made to map quantitative trait loci (QTLs) for yield traits using recombinant inbred lines (RIL). A genetic linkage map was constructed containing 609 loci, covering a total of 1557.48 cM with an average distance of 2.56 cM between adjacent markers. The present map exhibited good collinearity with the physical map of diploid species of Arachis. Ninety-two repeatable QTLs were identified for 11 traits including height of main stem, total branching number, and nine pod- and seed-related traits...
2017: Molecular Breeding: New Strategies in Plant Improvement
https://www.readbyqxmd.com/read/28215025/analysis-of-the-genetic-architecture-of-maize-ear-and-grain-morphological-traits-by-combined-linkage-and-association-mapping
#7
Chaoshu Zhang, Zhiqiang Zhou, Hongjun Yong, Xiaochong Zhang, Zhuanfang Hao, Fangjun Zhang, Mingshun Li, Degui Zhang, Xinhai Li, Zhenhua Wang, Jianfeng Weng
Using combined linkage and association mapping, 26 stable QTL and six stable SNPs were detected across multiple environments for eight ear and grain morphological traits in maize. One QTL, PKS2, might play an important role in maize yield improvement. In the present study, one bi-parental population and an association panel were used to identify quantitative trait loci (QTL) for eight ear and grain morphological traits. A total of 108 QTL related to these traits were detected across four environments using an ultra-high density bin map constructed using recombinant inbred lines (RILs) derived from a cross between Ye478 and Qi319, and 26 QTL were identified in more than two environments...
February 18, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28213629/transcriptome-based-snp-discovery-by-gbs-and-the-construction-of-a-genetic-map-for-olive
#8
Ahmet İpek, Meryem İpek, Sezai Ercişli, Nesrin Aktepe Tangu
Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique...
February 18, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28202046/highly-predictive-snp-markers-for-efficient-selection-of-the-wheat-leaf-rust-resistance-gene-lr16
#9
Mulualem T Kassa, Frank M You, Colin W Hiebert, Curtis J Pozniak, Pierre R Fobert, Andrew G Sharpe, James G Menzies, D Gavin Humphreys, Nicole Rezac Harrison, John P Fellers, Brent D McCallum, Curt A McCartney
BACKGROUND: Lr16 is a widely deployed leaf rust resistance gene in wheat (Triticum aestivum L.) that is highly effective against the North American Puccinia triticina population when pyramided with the gene Lr34. Lr16 is a seedling leaf rust resistance gene conditioning an incompatible interaction with a distinct necrotic ring surrounding the uredinium. Lr16 was previously mapped to the telomeric region of the short arm of wheat chromosome 2B. The goals of this study were to develop numerous single nucleotide polymorphism (SNP) markers for the Lr16 region and identify diagnostic gene-specific SNP marker assays for marker-assisted selection (MAS)...
February 15, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28193168/genome-wide-snp-identification-linkage-map-construction-and-qtl-mapping-for-seed-mineral-concentrations-and-contents-in-pea-pisum-sativum-l
#10
Yu Ma, Clarice J Coyne, Michael A Grusak, Michael Mazourek, Peng Cheng, Dorrie Main, Rebecca J McGee
BACKGROUND: Marker-assisted breeding is now routinely used in major crops to facilitate more efficient cultivar improvement. This has been significantly enabled by the use of next-generation sequencing technology to identify loci and markers associated with traits of interest. While rich in a range of nutritional components, such as protein, mineral nutrients, carbohydrates and several vitamins, pea (Pisum sativum L.), one of the oldest domesticated crops in the world, remains behind many other crops in the availability of genomic and genetic resources...
February 13, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28187136/candidate-genes-and-molecular-markers-associated-with-heat-tolerance-in-colonial-bentgrass
#11
David Jespersen, Faith C Belanger, Bingru Huang
Elevated temperature is a major abiotic stress limiting the growth of cool-season grasses during the summer months. The objectives of this study were to determine the genetic variation in the expression patterns of selected genes involved in several major metabolic pathways regulating heat tolerance for two genotypes contrasting in heat tolerance to confirm their status as potential candidate genes, and to identify PCR-based markers associated with candidate genes related to heat tolerance in a colonial (Agrostis capillaris L...
2017: PloS One
https://www.readbyqxmd.com/read/28184228/marker-aided-incorporation-of-saltol-a-major-qtl-associated-with-seedling-stage-salt-tolerance-into-oryza-sativa-pusa-basmati-1121
#12
N Naresh Babu, S Gopala Krishnan, K K Vinod, S L Krishnamurthy, Vivek K Singh, Madan P Singh, Renu Singh, Ranjith K Ellur, Vandna Rai, Haritha Bollinedi, Prolay K Bhowmick, Ashutosh K Yadav, Mariappan Nagarajan, Nagendra K Singh, Kumble V Prabhu, Ashok K Singh
Pusa Basmati 1121 (PB1121), an elite Basmati rice cultivar is vulnerable to salinity at seedling stage. A study was undertaken to impart seedling-stage salt tolerance into PB1121 by transferring a quantitative trait locus (QTL), Saltol, using FL478 as donor, through marker assisted backcrossing. Sequence tagged microsatellite site (STMS) marker RM 3412, tightly linked to Saltol was used for foreground selection. Background recovery was estimated using 90 genome-wide STMS markers. Systematic phenotypic selection helped in accelerated recovery of recurrent parent phenome (RPP)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28183791/appearance-of-qrs-fragmentation-late-after-mustard-senning-repair-is-associated-with-adverse-outcome
#13
Frederik Helsen, Bert Vandenberk, Pieter De Meester, Alexander Van De Bruaene, Charlien Gabriels, Els Troost, Marc Gewillig, Bart Meyns, Rik Willems, Werner Budts
OBJECTIVE: To evaluate if development of fragmented QRS (fQRS) complexes, a marker of inhomogeneous ventricular activation due to myocardial fibrosis, is associated with adverse outcome in adults after Mustard/Senning repair for d-transposition of the great arteries (d-TGA). METHODS: Adults with atrial switch repair for d-TGA were selected from the database of a tertiary care hospital. Exclusion criteria were systemic right ventricular (RV) assist device or heart transplantation (HTx) before the age of 16, or fQRS already present at first visit to the Adult Congenital Heart Disease clinic...
February 9, 2017: Heart: Official Journal of the British Cardiac Society
https://www.readbyqxmd.com/read/28177367/using-markers-with-large-effect-in-genetic-and-genomic-predictions
#14
M S Lopes, H Bovenhuis, M van Son, Ø Nordbø, E H Grindflek, E F Knol, J W M Bastiaansen
The first attempts of applying marker-assisted selection (MAS) in animal breeding were not very successful because the identification of markers closely linked to QTL using low-density microsatellite panels was difficult. More recently, the use of high-density SNP panels in genome-wide association studies (GWAS) have increased the power and precision of identifying markers linked to QTL, which offer new possibilities for MAS. However, when GWAS started to be performed, the focus of many breeders had already shifted from the use of MAS to the application of genomic selection (using all available markers without any preselection of markers linked to QTL)...
January 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28177053/the-use-of-microsatellite-markers-in-neotropical-studies-of-wild-birds-a-literature-review
#15
Renan F Moura, Deborah A Dawson, Denise M Nogueira
Despite extensive habitat fragmentation, the Neotropical region possesses 30% of the world´s bird species. Microsatellites have remained one of the most popular genetic markers and have been used in ecological and conservation studies since the 1990's. We conducted a literature review comparing the number of papers published from January 1990 to July 2015 that used microsatellite markers for studies of wild birds in the Neotropical region, USA and some European countries. We assigned the articles to three categories of studies: population genetics, animal behavior/kinship analysis and the development of species-specific bird microsatellite markers...
February 6, 2017: Anais da Academia Brasileira de Ciências
https://www.readbyqxmd.com/read/28176454/saturated-genic-snp-mapping-identified-functional-candidates-and-selection-tools-for-the-pinus-monticola-cr2-locus-controlling-resistance-to-white-pine-blister-rust
#16
Jun-Jun Liu, Richard A Sniezko, Arezoo Zamany, Holly Williams, Ning Wang, Angelia Kegley, Douglas P Savin, Hao Chen, Rona N Sturrock
Molecular breeding incorporates efficient tools to increase rust resistance in five-needle pines. Susceptibility of native five-needle pines to white pine blister rust (WPBR), caused by the non-native invasive fungus Cronartium ribicola (J.C.Fisch.), has significantly reduced wild populations of these conifers in North America. Major resistance (R) genes against specific avirulent pathotypes have been found in several five-needle pine species. In this study we screened genic SNP markers by comparative transcriptome and genetic association analyses and constructed saturated linkage maps for the western white pine (Pinus monticola) R locus (Cr2)...
February 7, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28173633/a-novel-functional-gene-associated-with-cold-tolerance-at-the-seedling-stage-in-rice
#17
Junliang Zhao, Shaohong Zhang, Jingfang Dong, Tifeng Yang, Xingxue Mao, Qing Liu, Xiaofei Wang, Bin Liu
Identification and cloning of cold-tolerant genes that can stably express under different cold environments are crucial for molecular rice breeding for cold tolerance. In the previous study, we identified a cold-tolerant QTL at the seedling stage, qCTS-9 which could be detected under different cold environments using a recombinant inbred line (RIL) population derived from a cold-tolerant variety Lijiangxintuanheigu (LTH) and a cold-sensitive variety Shanhuangzhan 2 (SHZ-2). In this study, eight candidate genes within the qCTS-9 interval were identified through integrated analysis of QTL mapping with genome-wide differential expression profiling of LTH...
February 7, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28164997/genome-wide-indel-ssr-scanning-reveals-significant-loci-associated-with-excellent-agronomic-traits-of-a-cabbage-brassica-oleracea-elite-parental-line-01-20
#18
Honghao Lv, Qingbiao Wang, Fengqing Han, Xing Liu, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yumei Liu, Zhansheng Li, Yangyong Zhang
Elite parental lines are of great significance to crop breeding. To discover unique genomic loci associated with excellent economic traits in the elite cabbage inbred-line '01-20', we performed comparisons of phenotypes as well as whole-genome insertion-deletion/simple sequence repeat loci between '01-20' and each of its five sister lines. '01-20' has a range of excellent agronomic traits, including early-maturing, and improvements in plant type and leaf colour. Eight unique loci were discovered for '01-20' and '01-07-258', another elite line similar to '01-20' at the whole-genome level...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28163599/development-and-validation-of-functional-caps-markers-for-the-fae-genes-in-brassica-juncea-and-their-use-in-marker-assisted-selection
#19
Navinder Saini, Naveen Singh, Anil Kumar, Nitika Vihan, Sangita Yadav, Sujata Vasudev, D K Yadava
Low erucic acid is a major breeding target to improve the edible oil quality in Brassica juncea. The single nucleotide polymorphism (SNP) in fatty acid elongase 1 (FAE1.1 and FAE1.2) gene was exploited to expedite the breeding program. The paralogs of FAE1 gene were sequenced from low erucic acid genotype Pusa Mustard 30 and SNPs were identified through homologous alignment with sequence downloaded from NCBI GenBank. Two SNPs in FAE1.1 at position 591 and 1265 and one in FAE1.2 at 237 were found polymorphic among low and high erucic acid genotypes...
December 2016: Breeding Science
https://www.readbyqxmd.com/read/28160079/development-and-dissection-of-diagnostic-snp-markers-for-the-downy-mildew-resistance-genes-pl-arg-and-pl-8-and-maker-assisted-gene-pyramiding-in-sunflower-helianthus-annuus-l
#20
L L Qi, Z I Talukder, B S Hulke, M E Foley
Diagnostic DNA markers are an invaluable resource in breeding programs for successful introgression and pyramiding of disease resistance genes. Resistance to downy mildew (DM) disease in sunflower is mediated by Pl genes which are known to be effective against the causal fungus, Plasmopara halstedii. Two DM resistance genes, Pl Arg and Pl 8 , are highly effective against P. halstedii races in the USA, and have been previously mapped to the sunflower linkage groups (LGs) 1 and 13, respectively, using simple sequence repeat (SSR) markers...
February 3, 2017: Molecular Genetics and Genomics: MGG
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