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Plant association mapping

Chenxia Liang, Gang Feng, Xingfeng Si, Lingfeng Mao, Guisheng Yang, Jens-Christian Svenning, Jie Yang
Bird species richness is mediated by local, regional, and historical factors, for example, competition, environmental heterogeneity, contemporary, and historical climate. Here, we related bird species richness with phylogenetic relatedness of bird assemblages, plant species richness, topography, contemporary climate, and glacial-interglacial climate change to investigate the relative importance of these factors. This study was conducted in Inner Mongolia, an arid and semiarid region with diverse vegetation types and strong species richness gradients...
January 2018: Ecology and Evolution
Zhiqiang Xia, Shengkui Zhang, Mingfu Wen, Cheng Lu, Yufang Sun, Meiling Zou, Wenquan Wang
Background: As an important biofuel plant, the demand for higher yield Jatropha curcas L. is rapidly increasing. However, genetic analysis of Jatropha and molecular breeding for higher yield have been hampered by the limited number of molecular markers available. Results: An ultrahigh-density linkage map for a Jatropha mapping population of 153 individuals was constructed and covered 1380.58 cM of the Jatropha genome, with average marker density of 0.403 cM. The genetic linkage map consisted of 3422 SNP and indel markers, which clustered into 11 linkage groups...
2018: Biotechnology for Biofuels
Minliang Jin, Xiangguo Liu, Wei Jia, Haijun Liu, Wenqiang Li, Yong Peng, Yanfang Du, Yuebin Wang, Yuejia Yin, Xuehai Zhang, Qing Liu, Min Deng, Nan Li, Xiyan Cui, Dongyun Hao, Jianbing Yan
Flowering time is a trait vital to the adaptation of flowering plants to different environments. Here, we report that CCT domain genes play an important role in flowering in maize (Zea mays L.). Among the 53 CCT family genes we identified in maize, 28 were located in flowering time quantitative trait locus regions and 15 were significantly associated with flowering time based on candidate-gene association mapping analysis. Furthermore, a CCT gene named ZmCOL3 was shown to be a repressor of flowering. Overexpressing ZmCOL3 delayed flowering time by approximately 4 days, in either long-day or short-day conditions...
January 10, 2018: Journal of Integrative Plant Biology
Xuewen Xu, Jing Ji, Qiang Xu, Xiaohua Qi, Yiqun Weng, Xuehao Chen
In plants, the formation of hypocotyl-derived adventitious roots (AR) is an important morphological acclimation to waterlogging stress; however, its genetic basis remains fragmentary. Here, through combined use of bulked segregant analysis-based whole genome sequencing, SNP haplotyping and fine genetic mapping, we identified a candidate gene for a major-effect QTL ARN6.1 that was responsible for waterlogging tolerance due to increased AR formation in the cucumber line Zaoer-N. Through multiple lines of evidence, we show that the CsARN6...
January 8, 2018: Plant Journal: for Cell and Molecular Biology
Aina E Prinzenberg, Marcela Víquez-Zamora, Jeremy Harbinson, Pim Lindhout, Sjaak van Heusden
Physiology and genetics are tightly interrelated. Understanding the genetic basis of a physiological trait such as the quantum yield of the photosystem II, or photosynthetic responses to environmental changes will benefit the understanding of these processes. By means of chlorophyll fluorescence imaging "CF", the quantum yield of photosystem II can be determined rapidly, precisely and non-invasively. In this article, the genetic control and variation in the steady-state quantum yield of PSII "ΦPSII " is analysed for diploid potato plants...
January 4, 2018: Physiologia Plantarum
Molla F Mengist, Sheila Alves, Denis Griffin, Joanne Creedon, Mike J McLaughlin, Peter W Jones, Dan Milbourne
Cd is a toxic metal, whilst Zn is an essential for plant and human health. Both can accumulate in potato tubers. We examine the genetic control of this process. The aim of this study was to map quantitative trait loci (QTLs) influencing tuber concentrations of cadmium (Cd) and zinc (Zn). We developed a segregating population comprising 188 F1 progeny derived from crossing two tetraploid cultivars exhibiting divergent tuber-Cd-accumulation phenotypes. These progeny were genotyped using the SolCap 8303 SNP array, and evaluated for Cd, Zn, and maturity-related traits...
January 6, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Raman Dhariwal, George Fedak, Yves Dion, Curtis Pozniak, André Laroche, François Eudes, Harpinder Singh Randhawa
Triticale (xTriticosecale Wittmack) is an important feed crop which suffers severe yield, grade and end-use quality losses due to Fusarium head blight (FHB). Development of resistant triticale cultivars is hindered by lack of effective genetic resistance sources. To dissect FHB resistance, a doubled haploid spring triticale population produced from the cross TMP16315/AC Ultima using a microspore culture method, was phenotyped for FHB incidence, severity, visual rating index (VRI), deoxynivalenol (DON) and some associated traits (ergot, grain protein content, test weight, yield, plant height and lodging) followed by single nucleotide polymorphism (SNP) genotyping...
January 5, 2018: Genes
Jason Abernathy, Ken Overturf
Reformulation of aquafeeds in salmonid diets to include more plant proteins is critical for sustainable aquaculture. However, increasing plant proteins can lead to stunted growth and enteritis. Toward an understanding of the regulatory mechanisms behind plant protein utilization, directional RNA sequencing of liver tissues from a rainbow trout strain selected for growth on an all plant-protein diet and a control strain, both fed a plant diet for 12 weeks, were utilized to construct long noncoding RNAs. Antisense long noncoding RNAs were selected for differential expression and functional analyses since they have been shown to have regulatory actions within a genome...
January 4, 2018: Animal Biotechnology
Omar Touhami, Jean Grégoire, Marie-Claude Renaud, Alexandra Sebastianelli, Katherine Grondin, Marie Plante
OBJECTIVES: To determine the risk of endometrial cancer (EC) and lymph node involvement in patients with a preoperative diagnosis of "AH-only" versus "AH - cannot rule out carcinoma" and to study the value of SLN mapping. METHODS: We reviewed all patients with a preoperative diagnosis of atypical hyperplasia, who underwent primary surgery with SLN mapping followed by pelvic lymphadenectomy. Sensitivity and negative predictive value (NPV) of SLN and rates of endometrial cancer were calculated...
December 28, 2017: Gynecologic Oncology
Mark W Jones, Bryan W Penning, Tiffany M Jamann, Jeff C Glaubitz, Cinta Romay, Edward S Buckler, Margaret Redinbaugh
The recent rapid emergence of maize lethal necrosis (MLN), caused by coinfection of maize with maize chlorotic mottle virus (MCMV) and a second virus usually from the family Potyviridae, is causing extensive losses for farmers in East Africa, Southeast Asia and South America. Although the genetic basis of resistance to potyviruses is well understood in maize, little was known about resistance to MCMV. The responses of five maize inbred lines (KS23-5, KS23-6, N211, DR and Oh1VI) to inoculation with MCMV, sugarcane mosaic virus and MLN were characterized...
December 29, 2017: Phytopathology
Agnieszka Golicz, Mohan B Singh, Prem L Bhalla
Long intergenic non-coding RNAs (lincRNAs) are emerging as important regulators of diverse biological processes. However, our understanding of lincRNA abundance and function remains very limited especially for agriculturally important plants. Soybean is a major legume crop plant providing over a half of global oilseed production. Moreover, soybean can form symbiotic relationships with Rhizobium bacteria to fix atmospheric nitrogen. Soybean has a complex paleopolyploid genome and exhibits many vegetative and floral development complexities...
December 28, 2017: Plant Physiology
Yi-Qun Gao, Jiu-Geng Chen, Zi-Ru Chen, Dong An, Qiao-Yan Lv, Mei-Ling Han, Ya-Ling Wang, David E Salt, Dai-Yin Chao
Ion homeostasis is essential for plant growth and environmental adaptation, and maintaining ion homeostasis requires the precise regulation of various ion transporters, as well as correct root patterning. However, the mechanisms underlying these processes remain largely elusive. Here, we reported that a choline transporter gene, CTL1, controls ionome homeostasis by regulating the secretory trafficking of proteins required for plasmodesmata (PD) development, as well as the transport of some ion transporters...
December 2017: PLoS Biology
Nabin Bhusal, Ashok Kumar Sarial, Pradeep Sharma, Sindhu Sareen
The current perspective of increasing global temperature makes heat stress as a major threat to wheat production worldwide. In order to identify quantitative trait loci (QTLs) associated with heat tolerance, 251 recombinant inbred lines (RILs) derived from a cross between HD2808 (heat tolerant) and HUW510 (heat susceptible) were evaluated under timely sown (normal) and late sown (heat stress) conditions for two consecutive crop seasons; 2013-14 and 2014-15. Grain yield (GY) and its components namely, grain weight/spike (GWS), grain number/spike (GNS), thousand grain weight (TGW), grain filling rate (GFR) and grain filling duration (GFD) were recorded for both conditions and years...
2017: PloS One
Cedric Wannaz, Peter Fantke, Olivier Jolliet
Exposure studies, used in human health risk and impact assessments of chemicals are largely performed locally or regionally. It is usually not known how global impacts resulting from exposure to point source emissions compare to local impacts. To address this problem, we introduce Pangea, an innovative multi-scale, spatial multimedia fate and exposure assessment model. We study local to global population exposure associated with emissions from 126 point sources matching locations of waste-to-energy plants across France...
December 18, 2017: Environmental Science & Technology
Javier Do Canto, Bruno Studer, Ursula Frei, Thomas Lübberstedt
A self-fertility locus was fine mapped to a 1.6 cM region on linkage group 5 in a perennial ryegrass population. This locus was the main determinant of pollen self-compatibility. In grasses, self-incompatibility (SI) is characterized by a two-loci gametophytic (S and Z) mechanism acting together in the recognition and inhibition of self-pollen. Mutations affecting the expression of SI have been reported in a few grass species. In perennial ryegrass (Lolium perenne L.), a mutation independent from S and Z, and mapping on linkage group 5 (LG 5), was previously reported to produce self-fertile plants...
December 15, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Carlton J Bequette, Sarah R Hind, Sarah Pulliam, Rebecca Higgins, Johannes W Stratmann
Plant responses to the environment and developmental processes are mediated by a complex signaling network. The Arabidopsis thaliana mitogen-activated protein kinases (MAPKs) MPK3 and MPK6 and their orthologs in other plants are shared signal transducers that respond to many developmental and environmental signals and thus represent highly connected hubs in the cellular signaling network. In animals, specific MAPK signaling complexes are assembled which enable input-specific protein-protein interactions and thus specific signaling outcomes...
December 12, 2017: Journal of Experimental Botany
Ryan R Lenz, Wenhao Dai
Phytoplasmas such as "Candidatus Phytoplasma pruni," the causal agent of X-disease of stone fruits, lack detailed biological analysis. This has limited the understanding of plant resistance mechanisms. Chokecherry (Prunus virginiana L.) is a promising model to be used for the plant-phytoplasma interaction due to its documented ability to resist X-disease infection. A consensus chokecherry genetic map "Cho" was developed with JoinMap 4.0 by joining two parental maps. The new map contains a complete set of 16 linkage groups, spanning a genetic distance of 2,172 cM with an average marker density of 3...
2017: Frontiers in Plant Science
Wen-Chieh Tsai, Anne Dievart, Chia-Chi Hsu, Yu-Yun Hsiao, Shang-Yi Chiou, Hsin Huang, Hong-Hwa Chen
Among 300,000 species in angiosperms, Orchidaceae containing 30,000 species is one of the largest families. Almost every habitats on earth have orchid plants successfully colonized, and it indicates that orchids are among the plants with significant ecological and evolutionary importance. So far, four orchid genomes have been sequenced, including Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen. Here, we review the current progress and the direction of orchid research in the post genomics era...
December 12, 2017: Botanical Studies (Taipei, Taiwan)
Mian Chee Gor, Chrishani Candappa, Thishakya de Silva, Nitin Mantri, Edwin Pang
Breeding strawberry (Fragaria x ananassa) with enhanced fruit flavour is one of the top breeding goals of many strawberry-producing countries. Although several genes involved in the biosynthetic pathways of key aroma compounds have been identified, the development and application of molecular markers associated with fruit flavour remain limited. This study aims to identify molecular markers closely linked to genes controlling strawberry aroma. A purpose-built Subtracted Diversity Array (SDA) known as Fragaria Discovery Panel (FDP) was used for marker screening...
December 12, 2017: Scientific Reports
Ruixiang Liu, Qingchang Meng, Fei Zheng, Lingjie Kong, Jianhua Yuan, Thomas Lübberstedt
Leaf width is an important component of plant architecture that affects light capture during photosynthesis and wind circulation under dense planting conditions. To improve understanding of the genetic mechanisms involved in leaf width at different positions, a comprehensive evaluation using the RIL (Recombinant Inbred Line) and IF2 (Immortalized F2) populations and a subsequent meta-analysis were performed. Forty-seven QTL associated with leaf width at different positions below the tassel were detected. The individual effects of QTL explained 3...
2017: PloS One
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