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https://www.readbyqxmd.com/read/28109190/qtl-mapping-and-candidate-genes-for-resistance-to-fusarium-ear-rot-and-fumonisin-contamination-in-maize
#1
Valentina Maschietto, Cinzia Colombi, Raul Pirona, Giorgio Pea, Francesco Strozzi, Adriano Marocco, Laura Rossini, Alessandra Lanubile
BACKGROUND: Fusarium verticillioides is a common maize pathogen causing ear rot (FER) and contamination of the grains with the fumonisin B1 (FB1) mycotoxin. Resistance to FER and FB1 contamination are quantitative traits, affected by environmental conditions, and completely resistant maize genotypes to the pathogen are so far unknown. In order to uncover genomic regions associated to reduced FER and FB1 contamination and identify molecular markers for assisted selection, an F2:3 population of 188 progenies was developed crossing CO441 (resistant) and CO354 (susceptible) genotypes...
January 21, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28108698/genome-wide-analysis-of-fatty-acid-desaturation-and-its-response-to-temperature
#2
Guillaume Menard, Jose Martin Moreno, Fiona Bryant, Olaya Munoz-Azcarate, Amélie A Kelly, Keywan Hassani-Pak, Smita Kurup, Peter J Eastmond
Plants modify the polyunsaturated fatty acid content of their membrane and storage lipids in order to adapt to changes in temperature. In developing seeds this response is largely controlled by the activities of the microsomal ω-6 and ω-3 fatty acid desaturases, FAD2 and FAD3. Although temperature-regulation of desaturation has been studied at the molecular and biochemical level, the genetic control of this trait is poorly understood. Here we have characterised the response of Arabidopsis thaliana seed lipids to variation in ambient temperature and found that heat inhibits both ω-6 and ω-3 desaturation in phosphatidylcholine, leading to a proportional change in triacylglycerol composition...
January 20, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28100189/an-snp-based-saturated-genetic-map-and-qtl-analysis-of-fruit-related-traits-in-zucchini-using-genotyping-by-sequencing
#3
Javier Montero-Pau, José Blanca, Cristina Esteras, Eva Ma Martínez-Pérez, Pedro Gómez, Antonio J Monforte, Joaquín Cañizares, Belén Picó
BACKGROUND: Cucurbita pepo is a cucurbit with growing economic importance worldwide. Zucchini morphotype is the most important within this highly variable species. Recently, transcriptome and Simple Sequence Repeat (SSR)- and Single Nucleotide Polymorphism (SNP)-based medium density maps have been reported, however further genomic tools are needed for efficient molecular breeding in the species. Our objective is to combine currently available complete transcriptomes and the Zucchini genome sequence with high throughput genotyping methods, mapping population development and extensive phenotyping to facilitate the advance of genomic research in this species...
January 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28100172/integrated-genomics-based-mapping-reveals-the-genetics-underlying-maize-flavonoid-biosynthesis
#4
Min Jin, Xuehai Zhang, Mingchao Zhao, Min Deng, Yuanhao Du, Yang Zhou, Shouchuang Wang, Takayuki Tohge, Alisdair R Fernie, Lothar Willmitzer, Yariv Brotman, Jianbing Yan, Weiwei Wen
BACKGROUND: Flavonoids constitute a diverse class of secondary metabolites which exhibit potent bioactivities for human health and have been indicated to play an important role in plant development and defense. However, accumulation and variation of flavonoid content in diverse maize lines and the genes responsible for their biosynthesis in this important crop remain largely unknown. In this study, we combine genetic mapping, metabolite profiling and gene regulatory network analysis to further enhance understanding of the maize flavonoid pathway...
January 18, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28100011/association-mapping-of-morphological-traits-in-wild-and-captive-zebra-finches-reliable-within-but-not-between-populations
#5
Ulrich Knief, Holger Schielzeth, Niclas Backström, Georg Hemmrich-Stanisak, Michael Wittig, Andre Franke, Simon C Griffith, Hans Ellegren, Bart Kempenaers, Wolfgang Forstmeier
Identifying causal genetic variants underlying heritable phenotypic variation is a longstanding goal in evolutionary genetics. We previously identified several quantitative trait loci (QTL) for five morphological traits in a captive population of zebra finches (Taeniopygia guttata) by whole-genome linkage mapping. We here follow up on these studies with the aim to narrow down on the quantitative trait variants (QTN) in one wild and three captive populations. First, we performed an association study using 672 single nucleotide polymorphisms (SNPs) within candidate genes located in the previously identified QTL regions in a sample of 939 wild-caught zebra finches...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28097398/mapping-quantitative-trait-loci-for-root-development-under-hypoxia-conditions-in-soybean-glycine-max-l-merr
#6
Loc Van Nguyen, Ryoji Takahashi, Stephen Mwangi Githiri, Tito O Rodriguez, Nobuko Tsutsumi, Sayuri Kajihara, Takasi Sayama, Masao Ishimoto, Kyuya Harada, Keisuke Suematsu, Tomomi Abiko, Toshihiro Mochizuki
Greatest potential, QTLs for hypoxia and waterlogging tolerance in soybean roots were detected using a new phenotypic evaluation method. Waterlogging is a major environmental stress limiting soybean yield in wet parts of the world. Root development is an important indicator of hypoxia tolerance in soybean. However, little is known about the genetic control of root development under hypoxia. This study was conducted to identify quantitative trait loci (QTLs) responsible for root development under hypoxia. Recombinant inbred lines (RILs) developed from a cross between a hypoxia-sensitive cultivar, Tachinagaha, and a tolerant landrace, Iyodaizu, were used...
January 17, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28093854/reduced-representation-genome-sequencing-reveals-patterns-of-genetic-diversity-and-selection-in-apple
#7
Baiquan Ma, Liao Liao, Qian Peng, Ting Fang, Hui Zhou, Schuyler S Korban, Yuepeng Han
Identifying DNA sequence variations is a fundamental step towards deciphering the genetic basis of traits of interest. Here, a total of 20 cultivated and 10 wild apples were genotyped using specific-locus amplified fragment sequencing, and 39,635 single nucleotide polymorphism with no missing genotypes and evenly distributed along the genome were selected to investigate patterns of genome-wide genetic variations between cultivated and wild apples. Overall, wild apples displayed higher levels of genetic diversity than cultivated apples...
January 17, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/28093083/genetic-analysis-of-teat-number-in-pigs-reveals-some-developmental-pathways-independent-of-vertebra-number-and-several-loci-which-only-affect-a-specific-side
#8
Gary A Rohrer, Dan J Nonneman
BACKGROUND: Number of functional teats is an important trait in commercial swine production. As litter size increases, the number of teats must also increase to supply nutrition to all piglets. Therefore, a genome-wide association analysis was conducted to identify genomic regions that affect this trait in a commercial swine population. Genotypic data from the Illumina Porcine SNP60v1 BeadChip were available for 2951 animals with total teat number (TTN) records. A subset of these animals (n = 1828) had number of teats on each side recorded...
January 4, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28088170/application-of-a-bayesian-dominance-model-improves-power-in-quantitative-trait-genome-wide-association-analysis
#9
Jörn Bennewitz, Christian Edel, Ruedi Fries, Theo H E Meuwissen, Robin Wellmann
BACKGROUND: Multi-marker methods, which fit all markers simultaneously, were originally tailored for genomic selection purposes, but have proven to be useful also in association analyses, especially the so-called BayesC Bayesian methods. In a recent study, BayesD extended BayesC towards accounting for dominance effects and improved prediction accuracy and persistence in genomic selection. The current study investigated the power and precision of BayesC and BayesD in genome-wide association studies by means of stochastic simulations and applied these methods to a dairy cattle dataset...
January 14, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28087756/fine-mapping-of-genes-determining-extrafusal-fiber-properties-in-murine-soleus-muscle
#10
Andrew Carroll, Riyan Cheng, Elaina Collie-Duguid, Caroline Meharg, Michael E Scholz, Steven N Fiering, Jennifer L Fields, Abraham A Palmer, Arimantas Lionikas
INTRODUCTION: Muscle fiber cross-sectional area (CSA) and proportion of different fiber types are important determinants of muscle function and overall metabolism. Genetic variation plays a substantial role in phenotypic variation of these traits, however, the underlying genes remain poorly understood. AIMS: This study aimed to map quantitative trait loci (QTL) affecting differences in soleus muscle fiber traits between the LG/J and SM/J mouse strains. METHODS: Fiber number, CSA, and proportion of oxidative type I fibers were assessed in the soleus of 334 genotyped male and female mice of the F34 generation of advanced intercross lines (AIL) derived from the LG/J and SM/J strains...
January 13, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28079294/a-locus-on-chromosome-16-is-significantly-associated-with-increased-tendency-to-lose-pups-in-females-of-the-rr-sgn-inbred-mouse-strain
#11
Jun-Ichi Suto
Females of the inbred mouse strain RR/Sgn have an apparent tendency to lose pups during rearing. To identify genes underlying this abnormal maternal phenotype, we performed quantitative trait loci (QTL) mapping in 349 (C57BL/6 J × RR/Sgn) F1  × RR/Sgn backcross mice and identified one significant and one suggestive QTL on chromosomes 16 and 4, respectively. We assigned the gene symbol nurturing ability QTL 3 (Naq3) to the QTL on chromosome 16. Twenty of the 21 mothers who lost entire litters were homozygous for RR/Sgn allele at Naq3; i...
November 2, 2016: Congenital Anomalies
https://www.readbyqxmd.com/read/28079141/development-of-a-690%C3%A2-k-snp-array-in-catfish-and-its-application-for-genetic-mapping-and-validation-of-the-reference-genome-sequence
#12
Qifan Zeng, Qiang Fu, Yun Li, Geoff Waldbieser, Brian Bosworth, Shikai Liu, Yujia Yang, Lisui Bao, Zihao Yuan, Ning Li, Zhanjiang Liu
Single nucleotide polymorphisms (SNPs) are capable of providing the highest level of genome coverage for genomic and genetic analysis because of their abundance and relatively even distribution in the genome. Such a capacity, however, cannot be achieved without an efficient genotyping platform such as SNP arrays. In this work, we developed a high-density SNP array with 690,662 unique SNPs (herein 690 K array) that were relatively evenly distributed across the entire genome, and covered 98.6% of the reference genome sequence...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28077090/gbs-based-single-dosage-markers-for-linkage-and-qtl-mapping-allow-gene-mining-for-yield-related-traits-in-sugarcane
#13
Thiago Willian Almeida Balsalobre, Guilherme da Silva Pereira, Gabriel Rodrigues Alves Margarido, Rodrigo Gazaffi, Fernanda Zatti Barreto, Carina Oliveira Anoni, Cláudio Benício Cardoso-Silva, Estela Araújo Costa, Melina Cristina Mancini, Hermann Paulo Hoffmann, Anete Pereira de Souza, Antonio Augusto Franco Garcia, Monalisa Sampaio Carneiro
BACKGROUND: Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection...
January 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28077071/an-integrated-analysis-of-qtl-mapping-and-rna-sequencing-provides-further-insights-and-promising-candidates-for-pod-number-variation-in-rapeseed-brassica-napus-l
#14
Jiang Ye, Yuhua Yang, Bo Chen, Jiaqin Shi, Meizhong Luo, Jiepeng Zhan, Xinfa Wang, Guihua Liu, Hanzhong Wang
BACKGROUND: As the most important yield component in rapeseed (Brassica napus L.), pod number is determined by a series of successive growth and development processes. Pod number shows extensive variation in rapeseed natural germplasm, which is valuable for genetic improvement. However, the genetic and especially the molecular mechanism for this kind of variation are poorly understood. In this study, we conducted QTL mapping and RNA sequencing, respectively, using the BnaZNRIL population and its two parental cultivars Zhongshuang11 and No...
January 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28070759/qtls-for-heading-date-and-plant-height-under-multiple-environments-in-rice
#15
Zhongmin Han, Wei Hu, Cong Tan, Yongzhong Xing
Both heading date and plant height are important traits related to grain yield in rice. In this study, a recombinant inbred lines (RILs) population was used to map quantitative trait loci (QTLs) for both traits under 3 long-day (LD) environments and 1 short-day (SD) environment. A total of eight QTLs for heading date and three QTLs for plant height were detected by composite interval mapping under LD conditions. Additional one QTL for heading date and three QTLs for plant height were identified by Two-QTL model under LD conditions...
January 9, 2017: Genetica
https://www.readbyqxmd.com/read/28068921/co-localization-of-major-quantitative-trait-loci-for-pod-size-and-weight-to-a-3-7%C3%A2-cm-interval-on-chromosome-a05-in-cultivated-peanut-arachis-hypogaea-l
#16
Huaiyong Luo, Xiaoping Ren, Zhendong Li, Zhijun Xu, Xinping Li, Li Huang, Xiaojing Zhou, Yuning Chen, Weigang Chen, Yong Lei, Boshou Liao, Manish K Pandey, Rajeev K Varshney, Baozhu Guo, Xiangguo Jiang, Fei Liu, Huifang Jiang
BACKGROUND: Cultivated peanut (Arachis hypogaea L.), an important source of edible oil and protein, is widely grown in tropical and subtropical areas of the world. Genetic improvement of yield-related traits is essential for improving yield potential of new peanut varieties. Genomics-assisted breeding (GAB) can accelerate the process of genetic improvement but requires linked markers for the traits of interest. In this context, we developed a recombinant inbred line (RIL) mapping population (Yuanza 9102 × Xuzhou 68-4) with 195 individuals and used to map quantitative trait loci (QTLs) associated with three important pod features, namely pod length, pod width and hundred-pod weight...
January 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28068919/construction-of-high-resolution-recombination-maps-in-asian-seabass
#17
Le Wang, Bin Bai, Peng Liu, Shu Qing Huang, Zi Yi Wan, Elaine Chua, Baoqing Ye, Gen Hua Yue
BACKGROUND: A high-density genetic map is essential for de novo genome assembly, fine mapping QTL for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution. Although a number of genomic resources are available in Asian seabass (Lates calcarifer), a high-density linkage map is still lacking. To facilitate QTL mapping for marker-assisted selection and genome assembly, and to understand the genome-wide recombination rates, we constructed high density linkage maps using three families and genotyping by sequencing...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28068426/screening-of-candidate-leaf-morphology-genes-by-integration-of-qtl-mapping-and-rna-sequencing-technologies-in-oilseed-rape-brassica-napus-l
#18
Hongju Jian, Bo Yang, Aoxiang Zhang, Li Zhang, Xinfu Xu, Jiana Li, Liezhao Liu
Leaf size and shape play important roles in agronomic traits, such as yield, quality and stress responses. Wide variations in leaf morphological traits exist in cultivated varieties of many plant species. By now, the genetics of leaf shape and size have not been characterized in Brassica napus. In this study, a population of 172 recombinant inbred lines (RILs) was used for quantitative trait locus (QTL) analysis of leaf morphology traits. Furthermore, fresh young leaves of extreme lines with more leaf lobes (referred to as 'A') and extreme lines with fewer lobes (referred to as 'B') selected from the RIL population and leaves of dissected lines (referred to as 'P') were used for transcriptional analysis...
2017: PloS One
https://www.readbyqxmd.com/read/28067953/complex-genetic-architecture-underlies-maize-tassel-domestication
#19
Guanghui Xu, Xufeng Wang, Cheng Huang, Dingyi Xu, Dan Li, Jinge Tian, Qiuyue Chen, Chenglong Wang, Yameng Liang, Yaoyao Wu, Xiaohong Yang, Feng Tian
Maize (Zea mays) tassels underwent profound morphological changes during maize domestication and improvement. Although a number of genes affecting maize inflorescence development have been identified, the genetic basis of the morphological changes in maize tassels since domestication is not well understood. Here, using a large population of 866 maize-teosinte BC2 S3 recombinant inbred lines genotyped using 19 838 single nucleotide polymorphism (SNP) markers, we performed high-resolution quantitative trait locus (QTL) mapping for five tassel morphological traits...
January 9, 2017: New Phytologist
https://www.readbyqxmd.com/read/28064191/novel-resampling-improves-statistical-power-for-multiple-trait-qtl-mapping
#20
Riyan Cheng, R W Doerge, Justin Borevitz
Multiple-trait analysis typically employs models that associate a quantitative trait locus (QTL) with all of the traits. As a result, statistical power for QTL detection may not be optimal if the QTL contributes to the phenotypic variation only in a small proportion of the traits. Excluding QTL effects that contribute little to the test statistic can improve statistical power. In this article, we show that an optimal power can be achieved when the number of QTL effects is best estimated and that a stringent criterion for QTL effect selection may improve power when the number of QTL effects is small but can reduce power otherwise...
January 6, 2017: G3: Genes—Genomes—Genetics
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