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Plant breeding

Yuanli Luo, Daiwen Dong, Yu Su, Xuyi Wang, Yumei Peng, Jiang Peng, Changyong Zhou
Mustard clubroot, caused by Plasmodiophora brassicae, is a serious disease that affects Brassica juncea var. tumida Tsen, a mustard plant that is the raw material for a traditional fermented food manufactured in Chongqing, China. In our laboratory, we screened the antagonistic bacteria Zhihengliuella aestuarii against P. brassicae. To better understand the biocontrol mechanism, three transcriptome analyses of B. juncea var. tumida Tsen were conducted using Illumina HiSeq 4000, one from B. juncea only inoculated with P...
March 22, 2018: Functional & Integrative Genomics
G J Ma, Q J Song, S G Markell, L L Qi
A novel rust resistance gene, R15 , derived from the cultivated sunflower HA-R8 was assigned to linkage group 8 of the sunflower genome using a genotyping-by-sequencing approach. SNP markers closely linked to R15 were identified, facilitating marker-assisted selection of resistance genes. The rust virulence gene is co-evolving with the resistance gene in sunflower, leading to the emergence of new physiologic pathotypes. This presents a continuous threat to the sunflower crop necessitating the development of resistant sunflower hybrids providing a more efficient, durable, and environmentally friendly host plant resistance...
March 21, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Gileung Lee, Kang-Ie Lee, Yunjoo Lee, Backki Kim, Dongryung Lee, Jeonghwan Seo, Su Jang, Joong Hyoun Chin, Hee-Jong Koh
The split-hull phenotype caused by reduced lemma width and low lignin content is under control of SPH encoding a type-2 13-lipoxygenase and contributes to high dehulling efficiency. Rice hulls consist of two bract-like structures, the lemma and palea. The hull is an important organ that helps to protect seeds from environmental stress, determines seed shape, and ensures grain filling. Achieving optimal hull size and morphology is beneficial for seed development. We characterized the split-hull (sph) mutant in rice, which exhibits hull splitting in the interlocking part between lemma and palea and/or the folded part of the lemma during the grain filling stage...
March 21, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Benjamin Stich, Delphine Van Inghelandt
Genomic prediction is a routine tool in breeding programs of most major animal and plant species. However, its usefulness for potato breeding has not yet been evaluated in detail. The objectives of this study were to (i) examine the prospects of genomic prediction of key performance traits in a diversity panel of tetraploid potato modeling additive, dominance, and epistatic effects, (ii) investigate the effects of size and make up of training set, number of test environments and molecular markers on prediction accuracy, and (iii) assess the effect of including markers from candidate genes on the prediction accuracy...
2018: Frontiers in Plant Science
Maria K Paulmann, Grit Kunert, Matthias R Zimmermann, Nina Theis, Anatoli Ludwig, Doreen Meichsner, Ralf Oelmüller, Jonathan Gershenzon, Antje Habekuss, Frank Ordon, Alexandra C U Furch, Torsten Will
Barley yellow dwarf virus (BYDV) is a phloem limited virus that is persistently transmitted by aphids. Due to huge yield losses in agriculture, the virus is of high economic relevance. Since the control of the virus itself is not possible, tolerant barley genotypes are considered as the most effective approach to avoid yield losses. Although several genes and quantitative trait loci are known and used in barley breeding for virus tolerance, little is known about molecular and physiological backgrounds of this trait...
2018: Frontiers in Plant Science
Katherine A Steele, Mark J Quinton-Tulloch, Resham B Amgai, Rajeev Dhakal, Shambhu P Khatiwada, Darshna Vyas, Martin Heine, John R Witcombe
Few public sector rice breeders have the capacity to use NGS-derived markers in their breeding programmes despite rapidly expanding repositories of rice genome sequence data. They rely on > 18,000 mapped microsatellites (SSRs) for marker-assisted selection (MAS) using gel analysis. Lack of knowledge about target SNP and InDel variant loci has hampered the uptake by many breeders of Kompetitive allele-specific PCR (KASP), a proprietary technology of LGC genomics that can distinguish alleles at variant loci...
2018: Molecular Breeding: New Strategies in Plant Improvement
Isidore A Diouf, Laurent Derivot, Frédérique Bitton, Laura Pascual, Mathilde Causse
Quality is a key trait in plant breeding, especially for fruit and vegetables. Quality involves several polygenic components, often influenced by environmental conditions with variable levels of genotype × environment interaction that must be considered in breeding strategies aiming to improve quality. In order to assess the impact of water deficit and salinity on tomato fruit quality, we evaluated a multi-parent advanced generation intercross (MAGIC) tomato population in contrasted environmental conditions over 2 years, one year in control vs...
2018: Frontiers in Plant Science
Washington Gapare, Shiming Liu, Warren Conaty, Qian-Hao Zhu, Vanessa Gillespie, Danny Llewellyn, Warwick Stiller, Iain Wilson
Genomic selection (GS) has successfully been used in plant breeding to improve selection efficiency and reduce breeding time and cost. However, there has not been a study to evaluate GS prediction models that may be used for predicting cotton breeding lines across multiple environments. In this study, we evaluated the performance of Bayes Ridge Regression, BayesA, BayesB, BayesC and Reproducing Kernel Hilbert Spaces regression models. We then extended the single-site GS model to accommodate genotype × environment interaction (G×E) in order to assess the merits of multi- over single-environment models in a practical breeding and selection context in cotton, a crop for which this has not previously been evaluated...
March 20, 2018: G3: Genes—Genomes—Genetics
C De La Fuente Canto, D I Kalogiros, M Ptashnyk, T S George, R Waugh, A G Bengough, J Russell, L X Dupuy
Discoveries on the genetics of resource acquisition efficiency are limited by the ability to measure plant roots in sufficient number and adequate genotypic variability. This paper presents a root phenotyping study that explores ways to combine live imaging and computer algorithms for model-based extraction of root growth parameters. The study is based on a subset of barley Recombinant Chromosome Substitution Lines (RCSLs) and a combinatorial approach was designed for fast identification of the regions of the genome that contribute the most to variations in root system architecture (RSA)...
March 17, 2018: Journal of Theoretical Biology
Cindy Wenke, Janina Pospiech, Tobias Reutter, Bettina Altmann, Uwe Truyen, Stephanie Speck
Biosecurity is defined as the implementation of measures that reduce the risk of disease agents being introduced and/or spread. For pig production, several of these measures are routinely implemented (e.g. cleaning, disinfection, segregation). However, air as a potential vector of pathogens has long been disregarded. Filters for incoming and recirculating air were installed into an already existing ventilation plant at a fattening piggery (3,840 pigs at maximum) in Saxony, Germany. Over a period of three consecutive fattening periods, we evaluated various parameters including air quality indices, environmental and operating parameters, and pig performance...
2018: PloS One
Xiaofen Zhang, Guoyun Wang, Bin Chen, Heshan Du, Fenglan Zhang, Haiying Zhang, Qian Wang, Sansheng Geng
First flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.), but the genetic mechanisms that control FFN are still poorly understood. In the present study, we developed 249 F2 plants derived from an intraspecific cross between the inbred pepper lines Z4 and Z5. Thirty plants with the highest FFN and 30 plants with the lowest FFN were chosen and their DNAs were pooled according to phenotype to construct two bulked DNA pools. Specific-locus amplified fragment sequencing (SLAF-seq) was combined with bulked segregant analysis (BSA) to identify candidate regions related to FFN...
2018: PloS One
Tobias Würschum, Guozheng Liu, Philipp H G Boeven, C Friedrich H Longin, Vilson Mirdita, Ebrahim Kazman, Yusheng Zhao, Jochen C Reif
The portfolio of available Reduced height loci (Rht-B1, Rht-D1, and Rht24) can be exploited for hybrid wheat breeding to achieve the desired heights in the female and male parents, as well as in the hybrids, without adverse effects on other traits relevant for hybrid seed production. Plant height is an important trait in wheat line breeding, but is of even greater importance in hybrid wheat breeding. Here, the height of the female and male parental lines must be controlled and adjusted relative to each other to maximize hybrid seed production...
March 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Erika Viljoen, Damaris A Odeny, Martin P A Coetzee, Dave K Berger, David J G Rees
Amaranthus species are an emerging and promising nutritious traditional vegetable food source. Morphological plasticity and poorly resolved dendrograms have led to the need for well resolved species phylogenies. We hypothesized that whole chloroplast phylogenomics would result in more reliable differentiation between closely related amaranth species. The aims of the study were therefore: to construct a fully assembled, annotated chloroplast genome sequence of Amaranthus tricolor; to characterize Amaranthus accessions phylogenetically by comparing barcoding genes (matK, rbcL, ITS) with whole chloroplast sequencing; and to use whole chloroplast phylogenomics to resolve deeper phylogenetic relationships...
March 19, 2018: Journal of Molecular Evolution
Francois Tardieu, Thierry Simonneau, Bertrand Muller
Drought tolerance involves mechanisms operating at different spatial and temporal scales, from rapid stomatal closure to maintenance of crop yield. We review how short-term mechanisms are controlled for stabilizing shoot water potential and how long-term processes have been constrained by evolution or breeding to fit into acclimation strategies for specific drought scenarios. These short- or long-term feedback processes participate in trade-offs between carbon accumulation and the risk of deleterious soil water depletion...
March 19, 2018: Annual Review of Plant Biology
Bing Wang, Steven M Smith, Jiayang Li
Shoot architecture is determined by the organization and activities of apical, axillary, intercalary, secondary, and inflorescence meristems and by the subsequent development of stems, leaves, shoot branches, and inflorescences. In this review, we discuss the unifying principles of hormonal and genetic control of shoot architecture including advances in our understanding of lateral branch outgrowth; control of stem elongation, thickness, and angle; and regulation of inflorescence development. We focus on recent progress made mainly in Arabidopsis thaliana, rice, pea, maize, and tomato, including the identification of new genes and mechanisms controlling shoot architecture...
March 19, 2018: Annual Review of Plant Biology
Hector Urbina, Martin F Breed, Weizhou Zhao, Kanaka Lakshmi Gurrala, Siv G E Andersson, Jon Ågren, Sandra Baldauf, Anna Rosling
Biotic and abiotic conditions in soil pose major constraints on growth and reproductive success of plants. Fungi are important agents in plant soil interactions but the belowground mycobiota associated with plants remains poorly understood. We grew one genotype each from Sweden and Italy of the widely-studied plant model Arabidopsis thaliana. Plants were grown under controlled conditions in organic topsoil local to the Swedish genotype, and harvested after ten weeks. Total DNA was extracted from three belowground compartments: endosphere (sonicated roots), rhizosphere and bulk soil, and fungal communities were characterized from each by amplification and sequencing of the fungal barcode region ITS2...
April 2018: Fungal Biology
Zhong-Feng Li, Yong Guo, Lin Ou, Huilong Hong, Jun Wang, Zhang-Xiong Liu, Bingfu Guo, Lijuan Zhang, Lijuan Qiu
GmDW1 encodes an ent-kaurene synthase (KS) acting at the early step of the biosynthesis pathway for gibberellins (GAs) and regulates the development of plant height in soybean. Plant height is an important component of plant architecture, and significantly affects crop breeding practices and yield. Here, we report the characterization of an EMS-induced dwarf mutant (dw) of the soybean cultivar Zhongpin 661 (ZDD23893). The dw mutant displayed reduced plant height and shortened internodes, both of which were mainly attributed to the longitudinally decreased cell length...
March 17, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Fengmei Shi, Yunhua Zhang, Keqin Wang, Qinglin Meng, Xinglong Liu, Ligong Ma, Yichu Li, Jia Liu, Ling Ma
Northern corn leaf blight (NCLB), caused by the hemibiotrophic fungal pathogen Setosphaeria turcica, is one of the major foliar diseases of maize. The use of resistant cultivars is the most effective, economical, and environmentally friendly means to control NCLB. At present, the molecular mechanisms of maize resistance to S. turcica is not clear. Elucidating the molecular resistance mechanisms of maize response to S. turcica would aid breeding for a maize variety with fungal tolerance. In this study, maize leaves before and after infection with S...
March 13, 2018: Gene
Abinaya Manivannan, Jin-Hee Kim, Eun-Young Yang, Yul-Kyun Ahn, Eun-Su Lee, Sena Choi, Do-Sun Kim
Pepper is an economically important horticultural plant that has been widely used for its pungency and spicy taste in worldwide cuisines. Therefore, the domestication of pepper has been carried out since antiquity. Owing to meet the growing demand for pepper with high quality, organoleptic property, nutraceutical contents, and disease tolerance, genomics assisted breeding techniques can be incorporated to develop novel pepper varieties with desired traits. The application of next-generation sequencing (NGS) approaches has reformed the plant breeding technology especially in the area of molecular marker assisted breeding...
2018: BioMed Research International
Abhinandan Mani Tripathi, Abhishek Niranjan, Sribash Roy
Development of flower color in plants is a complex process. Among others, it is an important trait for ornamental flowering plants. Canna is a flowering ornamental plant of family Cannaceae. To understand the molecular mechanism of flower color development in Canna, RNA sequencing from flower tissues of two contrasting flower color cultivars, Red President (RP) and Tropical Sunrise (TS) was performed. More than 27.0 million and 19.0 million clean reads were obtained from RP and TS, respectively. The combined clean reads were assembled into 147,295 unigenes...
March 7, 2018: Plant Physiology and Biochemistry: PPB
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