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Plant association mapping

Zhanfeng Si, Hui Liu, Jiankun Zhu, Jiedan Chen, Qiong Wang, Lei Fang, Fengkai Gao, Yue Tian, Yali Chen, Lijing Chang, Bingliang Liu, Zegang Han, Baoliang Zhou, Yan Hu, Xianzhong Huang, Tianzhen Zhang
In cotton, the formation of fruiting branches affects both plant architecture and fiber yield. Here, we report map-based cloning of the Gossypium barbadense axillary flowering (GbAF) mutation gene, which causes bolls to be borne directly on the main plant stem, and of the G. hirsutum clustered boll (cl1) mutation gene. Both mutant alleles were found to represent point mutations at the Cl1 locus of the corresponding species, and therefore we propose that the GbAF mutation be referred to as cl1b. These Cl1 loci correspond to homologs of tomato SELF-PRUNING (SP), i...
March 14, 2018: Journal of Experimental Botany
Zixiang Wen, Ruijuan Tan, Shichen Zhang, Paul J Collins, Jiazheng Yuan, Wenyan Du, Cuihua Gu, Shujun Ou, Qijian Song, Yong-Qiang Charles An, John F Boyse, Martin I Chilvers, Dechun Wang
White mold of soybean, caused by Sclerotinia sclerotiorum (Lib.) de Bary, is a necrotrophic fungus capable of infecting a wide range of plants. To dissect the genetic architecture of resistance to white mold, a high-density customized single nucleotide polymorphism (SNP) array (52,041 SNPs) was used to genotype two soybean diversity panels. Combined with resistance variation data observed in the field and greenhouse environments, genome-wide association studies (GWAS) were conducted to identify quantitative trait loci (QTL) controlling resistance against white mold...
March 12, 2018: Plant Biotechnology Journal
Wim Geeraerts, Vasileios Pothakos, Luc De Vuyst, Frédéric Leroy
Sliced cooked poultry products are susceptible to bacterial spoilage, notwithstanding their storage under modified-atmosphere packaging (MAP) in the cold chain. Although the prevailing bacterial communities are known to be mostly consisting of lactic acid bacteria (LAB), more information is needed about the potential variation in species diversity within national markets. In the present study, a total of 42 different samples of sliced cooked poultry products were collected in the Belgian retail and their bacterial communities were analysed at expiration date...
August 2018: Food Microbiology
Alessia Para, Ying Li, Gloria M Coruzzi
Chromatin immunoprecipitation (ChIP) is a widely used method to map the position of DNA-binding proteins such as histones and transcription factors (TFs) upon their interaction with particular regions of the genome. To examine the genomic distribution of a TF in specific cell types in response to a change in nitrogen concentration, we developed a micro-ChIP (μChIP) protocol that requires only ~5000 Arabidopsis cells transiently expressing the Arabidopsis TF Basic Leucine Zipper 1 (bZIP1) fused to the glucocorticoid receptor (GR) domain that mediates nuclear import in the presence of dexamethasone...
2018: Methods in Molecular Biology
Matthew W Blair, Andrés J Cortés, Andrew D Farmer, Wei Huang, Daniel Ambachew, R Varma Penmetsa, Noelia Carrasquilla-Garcia, Teshale Assefa, Steven B Cannon
Recombination (R) rate and linkage disequilibrium (LD) analyses are the basis for plant breeding. These vary by breeding system, by generation of inbreeding or outcrossing and by region in the chromosome. Common bean (Phaseolus vulgaris L.) is a favored food legume with a small sequenced genome (514 Mb) and n = 11 chromosomes. The goal of this study was to describe R and LD in the common bean genome using a 768-marker array of single nucleotide polymorphisms (SNP) based on Trans-legume Orthologous Group (TOG) genes along with an advanced-generation Recombinant Inbred Line reference mapping population (BAT93 x Jalo EEP558) and an internationally available diversity panel...
2018: PloS One
Heng Ye, Li Song, Huatao Chen, Babu Valliyodan, Liakat Ali, Tri Vuong, Chengjun Wu, John Orlowski, Blair Buckley, Pengyin Chen, J Grover Shannon, Henry T Nguyen
Natural genetic variations in waterlogging tolerance are controlled by multiple genes mapped as quantitative trait loci (QTL) in major crops, including soybean (Glycine max L.). In this research, two novel QTL associated with waterlogging tolerance were mapped from an elite/exotic soybean cross. The subsequent research was focused on a major QTL (qWT_Gm03) with the tolerant allele from the exotic parent. This QTL was isolated into near-isogenic backgrounds and its effects on waterlogging tolerance were validated in multiple environments...
March 8, 2018: Plant, Cell & Environment
Haoyang Xin, Tao Zhang, Yonghua Han, Yufeng Wu, Jisen Shi, Mengli Xi, Jiming Jiang
Dioecious species accounted for 6% of all plant species, including a number of crops and economically important species, such as poplar. However, sex determination and sex chromosome evolution have been studied only in few dioecious species. In poplar, the sex-determining locus was mapped to chromosome 19. Interestingly, this locus was mapped to either a peritelomeric or a centromeric region among different poplar species. We developed an oligonucleotide (oligo)-based chromosome painting probe based on the sequence of chromosome 19 from Populus trichocarpa...
March 8, 2018: Chromosoma
Ifeyinwa Onyemaobi, Habtamu Ayalew, Hui Liu, Kadambot H M Siddique, Guijun Yan
Grain number is a major trait for wheat yield under dryland farming. An International Triticeae Mapping Initiative (ITMI) mapping population comprising 105 recombinant inbred lines (RIL) developed from a cross between a Synthetic hexaploid wheat (Triticum aestivum) 'W7984' and a spring wheat variety 'Opata M85' was used to identify quantitative trait loci (QTL) associated with grain number per spike under two treatment conditions, normal watering and water stress during meiosis. Two major QTL for grain number per spike on the main stem Q...
2018: PloS One
Soumya Moonjely, Nemat O Keyhani, Michael J Bidochka
The hyd1/hyd2 hydrophobins are important constituents of the conidial cell wall of the insect pathogenic fungus Beauveria bassiana. This fungus can also form intimate associations with several plant species. Here, we show that inactivation of two Class I hydrophobin genes, hyd1 or hyd2, significantly decreases the interaction of B. bassiana with bean roots. Curiously, the ∆hyd1/∆hyd2 double mutant was less impaired in root association than Δhyd1 or Δhyd2. Loss of hyd genes affected growth rate, conidiation ability and oosporein production...
March 8, 2018: Microbiology
Yongle Li, Pradeep Ruperao, Jacqueline Batley, David Edwards, Tanveer Khan, Timothy D Colmer, Jiayin Pang, Kadambot H M Siddique, Tim Sutton
Drought tolerance is a complex trait that involves numerous genes. Identifying key causal genes or linked molecular markers can facilitate the fast development of drought tolerant varieties. Using a whole-genome resequencing approach, we sequenced 132 chickpea varieties and advanced breeding lines and found more than 144,000 single nucleotide polymorphisms (SNPs). We measured 13 yield and yield-related traits in three drought-prone environments of Western Australia. The genotypic effects were significant for all traits, and many traits showed highly significant correlations, ranging from 0...
2018: Frontiers in Plant Science
Khaled M Hazzouri, Basel Khraiwesh, Khaled M A Amiri, Duke Pauli, Tom Blake, Mohammad Shahid, Sangeeta K Mullath, David Nelson, Alain L Mansour, Kourosh Salehi-Ashtiani, Michael Purugganan, Khaled Masmoudi
Sodium (Na+ ) accumulation in the cytosol will result in ion homeostasis imbalance and toxicity of transpiring leaves. Studies of salinity tolerance in the diploid wheat ancestor Triticum monococcum showed that HKT1;5 -like gene was a major gene in the QTL for salt tolerance, named Nax2 . In the present study, we were interested in investigating the molecular mechanisms underpinning the role of the HKT1;5 gene in salt tolerance in barley ( Hordeum vulgare ). A USDA mini-core collection of 2,671 barley lines, part of a field trial was screened for salinity tolerance, and a Genome Wide Association Study (GWAS) was performed...
2018: Frontiers in Plant Science
Laiyuan Zhai, Tianqing Zheng, Xinyu Wang, Yun Wang, Kai Chen, Shu Wang, Yun Wang, Jianlong Xu, Zhikang Li
BACKGROUND: The vascular bundle especially in the peduncle is one of crucial limiting factors of rice yield, and it determines how plants efficiently transport photosynthetic products, mineral nutrients and water from leaf and root to panicle. However, the genetic base of rice vascular bundle related traits in the peduncle still remains unknown. RESULTS: The 423 panel showed substantial natural variations of peduncle vascular bundle. In total, 48 quantitative trait loci/locus (QTL) affecting the eight traits were identified throughout the genome by applying a significance threshold of P < 1...
March 6, 2018: Rice
M Saba Rahim, Himanshu Sharma, Afsana Parveen, Joy K Roy
Previously, association mapping (AM) methodology was used to unravel genetic complications in animal science by measuring the complex traits for candidate and non-candidate genes. Nowadays, this statistical approach is widely used to clarify the complexity in plant breeding program-based genome-wide breeding strategies, marker development, and diversity analysis. This chapter is particularly focused on methodologies with limitations and provides an overview of AM models and software used up to now. Association or linkage disequilibrium mapping has become a very popular method for discovering candidate and non-candidate genes and confirmation of quantitative trait loci (QTL) on various parts of the genome and in marker-assisted selection for breeding...
March 7, 2018: Advances in Biochemical Engineering/biotechnology
Uche Godfrey Okeke, Deniz Akdemir, Ismail Rabbi, Peter Kulakow, Jean-Luc Jannink
The HarvestPlus program for cassava ( Crantz) fortifies cassava with β-carotene by breeding for carotene-rich tubers (yellow cassava). However, a negative correlation between yellowness and dry matter (DM) content has been identified. We investigated the genetic control of DM in white and yellow cassava. We used regional heritability mapping (RHM) to associate DM with genomic segments in both subpopulations. Significant segments were subjected to candidate gene analysis and candidates were validated with prediction accuracies...
March 2018: Plant Genome
Renata de Castro Nunes, Simon Orozco-Arias, Dominique Crouzillat, Lukas A Mueller, Suzy R Strickler, Patrick Descombes, Coralie Fournier, Deborah Moine, Alexandre de Kochko, Priscila M Yuyama, André L L Vanzela, Romain Guyot
Centromeric regions of plants are generally composed of large array of satellites from a specific lineage of Gypsy LTR-retrotransposons, called Centromeric Retrotransposons. Repeated sequences interact with a specific H3 histone, playing a crucial function on kinetochore formation. To study the structure and composition of centromeric regions in the genus Coffea , we annotated and classified Centromeric Retrotransposons sequences from the allotetraploid C. arabica genome and its two diploid ancestors: Coffea canephora and C...
2018: Frontiers in Plant Science
Eleonora Barilli, María J Cobos, Estefanía Carrillo, Andrzej Kilian, Jason Carling, Diego Rubiales
Pisum fulvum , a wild relative of pea is an important source of allelic diversity to improve the genetic resistance of cultivated species against fungal diseases of economic importance like the pea rust caused by Uromyces pisi . To unravel the genetic control underlying resistance to this fungal disease, a recombinant inbred line (RIL) population was generated from a cross between two P. fulvum accessions, IFPI3260 and IFPI3251, and genotyped using Diversity Arrays Technology. A total of 9,569 high-quality DArT-Seq and 8,514 SNPs markers were generated...
2018: Frontiers in Plant Science
Shantel A Martinez, Jayfred Godoy, Meng Huang, Zhiwu Zhang, Arron H Carter, Kimberly A Garland Campbell, Camille M Steber
Preharvest sprouting (PHS), the germination of grain on the mother plant under cool and wet conditions, is a recurring problem for wheat farmers worldwide. α-amylase enzyme produced during PHS degrades starch resulting in baked good with poor end-use quality. The Hagberg-Perten Falling Number (FN) test is used to measure this problem in the wheat industry, and determines how much a farmer's wheat is discounted for PHS damage. PHS tolerance is associated with higher grain dormancy. Thus, breeding programs use germination-based assays such as the spike-wetting test to measure PHS susceptibility...
2018: Frontiers in Plant Science
Anita Tripathi, Osmani Chacon, Sneh Lata Singla-Pareek, Sudhir K Sopory, Neeti Sanan-Mishra
In the recent years, glyoxalase pathway has been an active area of research in both human and plants. This pathway is reported to confer stress tolerance in plants, by modulating the glutathione homeostasis to achieve detoxification of a potent cytotoxic and mutagenic compound, methylglyoxal. The microRNAs (miRNAs) are also reported to play significant role in stress tolerance for plants. However, the cross-talk of miRNAs with the metabolism regulated by glyoxalase in the salinity-tolerance is unexplored. We therefore investigated whether expression profiles of miRNAs are altered in response to glyoxalase overexpression, and if any of these are also responsible for modulating the stress responses of plants...
January 2018: Current Genomics
Andrea Oliveira Dias Temponi, Mariana Gontijo de Brito, Marcela Lencine Ferraz, Soraia de Araújo Diniz, Marcos Xavier Silva, Tarcísio Neves da Cunha
The aim of this study was to explain the association between social-environmental factors and major land uses and the occurrence of cases of American tegumentary leishmaniasis (ATL) in the spatial circuits of production in Minas Gerais State, Brazil. This was an analytical-type ecological study based on secondary data on ATL divided by three-year period from 2007 to 2011, in which the analytical units were municipalities belonging to the spatial circuits. Two distinct stages were performed. The first was the elaboration of thematic maps with identification of the circuits...
February 19, 2018: Cadernos de Saúde Pública
Jihong Zhang, Li Zeng, Shaoyang Chen, Helong Sun, Shuang Ma
Salinity stress can impede development and plant growth adversely. However, there is very little molecular information on NaCl resistance and volatile emissions in Lycopersicum esculentum. In order to investigate the effects of salt stress on the release of volatile compounds, we quantified and compared transcriptome changes by RNA-Seq analysis and volatile constituents with gas chromatography/mass spectrometry (GC/MS) coupled with solid-phase microextraction (SPME) after exposure to continuous salt stress...
February 17, 2018: Plant Physiology and Biochemistry: PPB
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