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Molecular Breeding: New Strategies in Plant Improvement

Shalabh Dixit, Anshuman Singh, Nitika Sandhu, Aditi Bhandari, Prashant Vikram, Arvind Kumar
TDK1 is a popular rice variety from the Lao PDR. Originally developed for irrigated conditions, this variety suffers a high decline in yield under drought conditions. Studies have identified three quantitative trait loci (QTLs) for grain yield under drought conditions, qDTY3.1 , qDTY6.1 , and qDTY6.2 , that show a high effect in the background of this variety. We report here the pyramiding of these three QTLs with SUB1 that provides 2-3 weeks of tolerance to complete submergence, with the aim to develop drought- and submergence-tolerant near-isogenic lines (NILs) of TDK1...
2017: Molecular Breeding: New Strategies in Plant Improvement
Eduardo Cruz-Rus, Rafael Sesmero, José A Ángel-Pérez, José F Sánchez-Sevilla, Detlef Ulrich, Iraida Amaya
Flavor improvement is currently one of the most important goals for strawberry breeders. At the same time, it is one of the most complex traits to improve, involving the balanced combination of several desired characteristics such as high sweetness, moderate acidity, and the appropriate combination of aroma compounds that are beginning to be delineated in consumer tests. DNA-informed breeding will expedite the selection of complex traits, such as flavor, over traditional phenotypic evaluation, particularly when markers linked to several traits of interests are combined during the breeding process...
2017: Molecular Breeding: New Strategies in Plant Improvement
Jiayin Song, Brett F Carver, Carol Powers, Liuling Yan, Jaroslav Klápště, Yousry A El-Kassaby, Charles Chen
Crop improvement is a long-term, expensive institutional endeavor. Genomic selection (GS), which uses single nucleotide polymorphism (SNP) information to estimate genomic breeding values, has proven efficient to increasing genetic gain by accelerating the breeding process in animal breeding programs. As for crop improvement, with few exceptions, GS applicability remains in the evaluation of algorithm performance. In this study, we examined factors related to GS applicability in line development stage for grain yield using a hard red winter wheat (Triticum aestivum L...
2017: Molecular Breeding: New Strategies in Plant Improvement
María-Dolores Rey, Azahara C Martín, Janet Higgins, David Swarbreck, Cristobal Uauy, Peter Shaw, Graham Moore
Despite possessing related ancestral genomes, hexaploid wheat behaves as a diploid during meiosis. The wheat Ph1 locus promotes accurate synapsis and crossover of homologous chromosomes. Interspecific hybrids between wheat and wild relatives are exploited by breeders to introgress important traits from wild relatives into wheat, although in hybrids between hexaploid wheat and wild relatives, which possess only homoeologues, crossovers do not take place during meiosis at metaphase I. However, in hybrids between Ph1 deletion mutants and wild relatives, crossovers do take place...
2017: Molecular Breeding: New Strategies in Plant Improvement
Jiemeng Xu, Nicky Driedonks, Marc J M Rutten, Wim H Vriezen, Gert-Jan de Boer, Ivo Rieu
Global warming has become a worldwide concern due to its adverse effects on agricultural output. In particular, long-term mildly high temperatures interfere with sexual reproduction and thus fruit and seed set. To uncover the genetic basis of observed variation in tolerance against heat, a bi-parental F2 mapping population from two contrasting cultivars, i.e. Nagcarlang and NCHS-1, was generated and phenotyped under continuous mild heat conditions for a number of traits underlying reproductive success, i.e...
2017: 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
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