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Molecular Breeding: New Strategies in Plant Improvement

F K S Yeo, R Bouchon, R Kuijken, A Loriaux, C Boyd, R E Niks, T C Marcel
Partial resistance quantitative trait loci (QTLs) Rphq11 and rphq16 against Puccinia hordei isolate 1.2.1 were previously mapped in seedlings of the mapping populations Steptoe/Morex and Oregon Wolfe Barleys, respectively. In this study, QTL mapping was performed at adult plant stage for the two mapping populations challenged with the same rust isolate. The results suggest that Rphq11 and rphq16 are effective only at seedling stage, and not at adult plant stage. The cloning of several genes responsible for partial resistance of barley to P...
2017: Molecular Breeding: New Strategies in Plant Improvement
María-Dolores Rey, Pilar Prieto
Simple, reliable methods for the identification of alien genetic introgressions are required in plant breeding programmes. The use of genomic dot-blot hybridisation allows the detection of small Hordeum chilense genomic introgressions in the descendants of genetic crosses between wheat and H. chilense addition or substitution lines in wheat when molecular markers are difficult to use. Based on genomic in situ hybridisation, DNA samples from wheat lines carrying putatively H. chilense introgressions were immobilised on a membrane, blocked with wheat genomic DNA and hybridised with biotin-labelled H...
2017: Molecular Breeding: New Strategies in Plant Improvement
Cheng Xu, Yonghong Ren, Yinqiao Jian, Zifeng Guo, Yan Zhang, Chuanxiao Xie, Junjie Fu, Hongwu Wang, Guoying Wang, Yunbi Xu, Ping Li, Cheng Zou
With the decrease of cost in genotyping, single nucleotide polymorphisms (SNPs) have gained wide acceptance because of their abundance, even distribution throughout the maize (Zea mays L.) genome, and suitability for high-throughput analysis. In this study, a maize 55 K SNP array with improved genome coverage for molecular breeding was developed on an Affymetrix® Axiom® platform with 55,229 SNPs evenly distributed across the genome, including 22,278 exonic and 19,425 intronic SNPs. This array contains 451 markers that are associated with 368 known genes and two traits of agronomic importance (drought tolerance and kernel oil biosynthesis), 4067 markers that are not covered by the current reference genome, 734 markers that are differentiated significantly between heterotic groups, and 132 markers that are tags for important transgenic events...
2017: Molecular Breeding: New Strategies in Plant Improvement
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
Yiqian Fu, Alex van Silfhout, Arwa Shahin, Ronny Egberts, Martin Beers, Ans van der Velde, Adrie van Houten, Jaap M van Tuyl, Richard G F Visser, Paul Arens
Gerbera hybrida is an economically important cut flower. In the production and transportation of gerbera with unavoidable periods of high relative humidity, grey mould occurs and results in losses in quality and quantity of flowers. Considering the limitations of chemical use in greenhouses and the impossibility to use these chemicals in auction or after sale, breeding for resistant gerbera cultivars is considered as the best practical approach. In this study, we developed two segregating F1 populations (called S and F)...
2017: Molecular Breeding: New Strategies in Plant Improvement
Goettel Wolfgang, Yong-Qiang Charles An
North American soybean breeders have successfully developed a large number of elite cultivars with diverse maturity groups (MG) from a small number of ancestral landraces. To understand molecular and genetic basis underlying the large variation in their maturity and flowering times, we integrated pedigree and maturity data of 166 cultivars representing North American soybean breeding. Network analysis and visualization of their pedigree relationships revealed a clear separation of southern and northern soybean breeding programs, suggesting that little genetic exchange occurred between northern (MG 0-IV) and southern cultivars (MG V-VIII)...
2017: Molecular Breeding: New Strategies in Plant Improvement
Stefano Pessina, Luisa Palmieri, Luca Bianco, Jennifer Gassmann, Eric van de Weg, Richard G F Visser, Pierluigi Magnago, Henk J Schouten, Yuling Bai, R Riccardo Velasco, Mickael Malnoy
Podosphaera leucotricha is the causal agent of powdery mildew (PM) in apple. To reduce the amount of fungicides required to control this pathogen, the development of resistant apple cultivars should become a priority. Resistance to PM was achieved in various crops by knocking out specific members of the MLO gene family that are responsible for PM susceptibility (S-genes). In apple, the knockdown of MdMLO19 resulted in PM resistance. However, since gene silencing technologies such as RNAi are perceived unfavorably in Europe, a different approach that exploits this type of resistance is needed...
2017: Molecular Breeding: New Strategies in Plant Improvement
Soon Li Teh, Jonathan Fresnedo-Ramírez, Matthew D Clark, David M Gadoury, Qi Sun, Lance Cadle-Davidson, James J Luby
Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis) breeding program, although experimental families are typically unreplicated, the genetic backgrounds may contain similar progenitors previously selected due to their contribution of favorable alleles. In this study, we investigated the utility of joint QTL identification provided by analyzing half-sib families...
2017: Molecular Breeding: New Strategies in Plant Improvement
Peter G Walley, Gemma Hough, Jonathan D Moore, John Carder, Marian Elliott, Andrew Mead, Julie Jones, Graham Teakle, Guy Barker, Vicky Buchanan-Wollaston, Paul Hand, David Pink, Rosemary Collier
Domesticated lettuce varieties encompass much morphological variation across a range of crop type groups, with large collections of cultivars and landrace accessions maintained in genebanks. Additional variation not captured during domestication, present in ancestral wild relatives, represents a potentially rich source of alleles that can deliver to sustainable crop production. However, these large collections are difficult and costly to screen for many agronomically important traits. In this paper, we describe the generation of a diversity collection of 96 lettuce and wild species accessions that are amenable to routine phenotypic analysis and their genotypic characterization with a panel of 682 newly developed expressed sequence tag (EST)-linked KASP™ single nucleotide polymorphism (SNP) markers that are anchored to the draft Lactuca sativa genome assembly...
2017: Molecular Breeding: New Strategies in Plant Improvement
Corey J Lees, Genyi Li, Robert W Duncan
Identifying parental combinations that exhibit high heterosis is a constant target for commercial Brassica napus L. hybrid development programs. Finding high heterotic parental combinations can require hundreds of test crosses and years of yield evaluation. Heterotic pool development could be used to divide breeding material into specific breeding pools and focus the number of parental combinations created. Here, we report the genotypic characterization of 79 B. napus genotypes by calculating genetic distance based on sequence-related amplified polymorphism (SRAP) and genotyping by sequencing (GBS) in association with a neighbour-joining clustering algorithm...
2016: Molecular Breeding: New Strategies in Plant Improvement
Wirulda Pootakham, Chutima Sonthirod, Chaiwat Naktang, Nukoon Jomchai, Duangjai Sangsrakru, Sithichoke Tangphatsornruang
Advances in next generation sequencing have facilitated a large-scale single nucleotide polymorphism (SNP) discovery in many crop species. Genotyping-by-sequencing (GBS) approach couples next generation sequencing with genome complexity reduction techniques to simultaneously identify and genotype SNPs. Choice of enzymes used in GBS library preparation depends on several factors including the number of markers required, the desired level of multiplexing, and whether the enrichment of genic SNP is preferred. We evaluated various combinations of methylation-sensitive (AatII, PstI, MspI) and methylation-insensitive (SphI, MseI) enzymes for their effectiveness in genome complexity reduction and enrichment of genic SNPs...
2016: Molecular Breeding: New Strategies in Plant Improvement
Benjamin Dubois, Pierre Bertin, Dominique Mingeot
The gluten proteins of cereals such as bread wheat (Triticum aestivum ssp. aestivum) and spelt (T. aestivum ssp. spelta) are responsible for celiac disease (CD). The α-gliadins constitute the most immunogenic class of gluten proteins as they include four main T-cell stimulatory epitopes that affect CD patients. Spelt has been less studied than bread wheat and could constitute a source of valuable diversity. The objective of this work was to study the genetic diversity of spelt α-gliadin transcripts and to compare it with those of bread wheat...
2016: Molecular Breeding: New Strategies in Plant Improvement
Y Wang, X L Wang, J Y Meng, Y J Zhang, Z H He, Y Yang
Wheat grain color does not only affect the brightness of flour but also seed dormancy and pre-harvest sprouting (PHS) tolerance. The transcription factor Tamyb10 is an important candidate for R-1 gene, and the expression of its homologs determines wheat seed coat color. In the present study, the allelic variations of Tamyb10 were explored in a set of Chinese bread wheat varieties and advanced lines with different PHS tolerance, and a sequenced-tagged site (STS) marker for Tamyb10-D1 gene was developed, designated as Tamyb10D, which could be used as an efficient and reliable marker to evaluate the depth dormancy of wheat seeds...
2016: Molecular Breeding: New Strategies in Plant Improvement
Virginia W Gitonga, Robert Stolker, Carole F S Koning-Boucoiran, Mitra Aelaei, Richard G F Visser, Chris Maliepaard, Frans A Krens
The success of cut rose cultivars is a direct result of their aesthetic value. The rose industry thrives on novelty, and the production of novel flower color has been extensively studied. The most popular color is red, and it is, therefore, important for breeders to produce a good red cultivar. The final visible color of the flower is a combination of a number of factors including the type of anthocyanin accumulating, modifications to the anthocyanidin molecule, co-pigmentation and vacuolar pH. Here, we analyze the quantitative variation of the biochemical constituents of flower color in a tetraploid rose population and combine this with marker information in the segregating rose population to map the chromosomal locations of putative QTLs for flower color traits...
2016: Molecular Breeding: New Strategies in Plant Improvement
Roeland E Voorrips, Marco C A M Bink, Johannes W Kruisselbrink, Herma J J Koehorst-van Putten, W Eric van de Weg
In the study of large outbred pedigrees with many founders, individual bi-allelic markers, such as SNP markers, carry little information. After phasing the marker genotypes, multi-allelic loci consisting of groups of closely linked markers can be identified, which are called "haploblocks". Here, we describe PediHaplotyper, an R package capable of assigning consistent alleles to such haploblocks, allowing for missing and incorrect SNP data. These haploblock genotypes are much easier to interpret by the human investigator than the original SNP data and also allow more efficient QTL analyses that require less memory and computation time...
2016: Molecular Breeding: New Strategies in Plant Improvement
Yansong Ma, Jochen C Reif, Yong Jiang, Zixiang Wen, Dechun Wang, Zhangxiong Liu, Yong Guo, Shuhong Wei, Shuming Wang, Chunming Yang, Huicai Wang, Chunyan Yang, Weiguo Lu, Ran Xu, Rong Zhou, Ruizhen Wang, Zudong Sun, Huaizhu Chen, Wanhai Zhang, Jian Wu, Guohua Hu, Chunyan Liu, Xiaoyan Luan, Yashu Fu, Tai Guo, Tianfu Han, Mengchen Zhang, Bincheng Sun, Lei Zhang, Weiyuan Chen, Cunxiang Wu, Shi Sun, Baojun Yuan, Xinan Zhou, Dezhi Han, Hongrui Yan, Wenbin Li, Lijuan Qiu
Genomic selection is a promising molecular breeding strategy enhancing genetic gain per unit time. The objectives of our study were to (1) explore the prediction accuracy of genomic selection for plant height and yield per plant in soybean [Glycine max (L.) Merr.], (2) discuss the relationship between prediction accuracy and numbers of markers, and (3) evaluate the effect of marker preselection based on different methods on the prediction accuracy. Our study is based on a population of 235 soybean varieties which were evaluated for plant height and yield per plant at multiple locations and genotyped by 5361 single nucleotide polymorphism markers...
2016: Molecular Breeding: New Strategies in Plant Improvement
Sanjaya Gyawali, Myrtle Harrington, Jonathan Durkin, Kyla Horner, Isobel A P Parkin, Dwayne D Hegedus, Diana Bekkaoui, Lone Buchwaldt
The fungal pathogen Sclerotinia sclerotiorum causes stem rot of oilseed rape (Brassica napus) worldwide. In preparation for genome-wide association mapping (GWAM) of sclerotinia resistance in B. napus, 152 accessions from diverse geographical regions were screened with a single Canadian isolate, #321. Plants were inoculated by attaching mycelium plugs to the main stem at full flower. Lesion lengths measured 7, 14 and 21 days after inoculation were used to calculate the area under the disease progress curve (AUDPC)...
2016: Molecular Breeding: New Strategies in Plant Improvement
Weijun Ye, Shikai Hu, Liwen Wu, Changwei Ge, Yongtao Cui, Ping Chen, Xiaoqi Wang, Jie Xu, Deyong Ren, Guojun Dong, Qian Qian, Longbiao Guo
Chloroplast is a crucial organelle for plant photosynthesis and maintaining normal life activities in higher plants. Although some genes related to chloroplast development and pigment synthesis have been identified or cloned in rice, little is known about the relationship between these genes and abiotic stress response. In this study, we identified a novel mutant white stripe leaf 12 (wsl12) affecting pigment synthesis, chloroplast development and abiotic stress response in rice. The mutant phenotype was obvious at seeding and tillering stages and in response to the temperature change...
2016: Molecular Breeding: New Strategies in Plant Improvement
Bjarne Larsen, Marian Ørgaard, Torben Bo Toldam-Andersen, Carsten Pedersen
We present a new efficient screening tool for detection of S-alleles in apple. The protocol using general and multiplexed primers for PCR reaction and fragment detection on an automatized capillary DNA sequencer exposed a higher number of alleles than any previous studies. Analysis of alleles is made on basis of three individual fragment sizes making the allele interpretation highly accurate. The method was employed to genotype 432 Malus accessions and exposed 25 different S-alleles in a selection of Malus domestica cultivars of mainly Danish origin (402 accessions) as well as a selection of other Malus species (30 accessions)...
2016: Molecular Breeding: New Strategies in Plant Improvement
Yongli Zhao, Chong Zhang, Hua Chen, Mei Yuan, Rick Nipper, C S Prakash, Weijian Zhuang, Guohao He
Bacterial wilt (BW) caused by Ralstonia solanacearum is a serious, global, disease of peanut (Arachis hypogaea L.), but it is especially destructive in China. Identification of DNA markers linked to the resistance to this disease will help peanut breeders efficiently develop resistant cultivars through molecular breeding. A F2 population, from a cross between disease-resistant and disease-susceptible cultivars, was used to detect quantitative trait loci (QTL) associated with the resistance to this disease in the cultivated peanut...
2016: Molecular Breeding: New Strategies in Plant Improvement
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