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Plant chromosomes

Martine Boccara, Alexis Sarazin, Bernard Billoud, Agnes Bulski, Louise Chapell, David Baulcombe, Vincent Colot
Epigenetic response to stress in plants involves changes in DNA methylation, histone modifications, and expression of small noncoding RNAs (sRNA). Here we present the method of analysis of differential expression of sRNA populations using DNA tiling arrays. sRNA extracted from Arabidopsis thaliana plants exposed to pathogen elicitor or control plants were reverse-transcribed into cDNAs, and subsequently hybridized after labeling to a custom-made DNA tiling array covering Arabidopsis chromosome 4. We first designed a control experiment with eight cDNA clones corresponding to sequences located on chromosome 4 and obtained robust and specific hybridization signals...
2017: Methods in Molecular Biology
Stefan Grob, Ueli Grossniklaus
Nuclear organization and higher-order chromosome structure in interphase nuclei are thought to have important effects on fundamental biological processes, including chromosome condensation, replication, and transcription. Until recently, however, nuclear organization could only be analyzed microscopically. The development of chromatin conformation capture (3C)-based techniques now allows a detailed look at chromosomal architecture from the level of individual loci to the entire genome. Here we provide a robust Hi-C protocol, allowing the analysis of nuclear organization in nuclei from different wild-type and mutant plant tissues...
2017: Methods in Molecular Biology
Kohtaro Watanabe, Hirokazu Takahashi, Saori Sato, Shunsaku Nishiuchi, Fumie Omori, Al Imran Malik, Timothy David Colmer, Yoshiro Mano, Mikio Nakazono
A radial oxygen loss (ROL) barrier in roots of waterlogging-tolerant plants promotes oxygen movement via aerenchyma to the root tip, and impedes soil phytotoxin entry. The molecular mechanism and genetic regulation of ROL barrier formation are largely unknown. Zea nicaraguensis, a waterlogging-tolerant wild relative of maize (Z. mays ssp. mays), forms a tight ROL barrier in its roots when waterlogged. We used Z. nicaraguensis chromosome segment introgression lines (ILs) in maize (inbred line Mi29) to elucidate the chromosomal region involved in regulating root ROL barrier formation...
October 20, 2016: Plant, Cell & Environment
Garrett J McKinney, Ryan K Waples, Lisa W Seeb, James E Seeb
Whole genome duplications have occurred in the recent ancestors of many plants, fish, and amphibians, resulting in a pervasiveness of paralogous loci and the potential for both disomic and tetrasomic inheritance in the same genome. Paralogs can be difficult to reliably genotype and are often excluded from genotyping-by-sequencing (GBS) analyses; however, removal requires paralogs to be identified which is difficult without a reference genome. We present a method for identifying paralogs in natural populations by combining two properties of duplicated loci: 1) the expected frequency of heterozygotes exceeds that for singleton loci, and 2) within heterozygotes, observed read ratios for each allele in GBS data will deviate from the 1:1 expected for singleton (diploid) loci...
October 19, 2016: Molecular Ecology Resources
Dekai Wang, Heqin Liu, Guowei Zhai, Liangsheng Wang, Jianfeng Shao, Yuezhi Tao
Functional chloroplast generation depends on the precise coordination of gene expression between the plastid and the nucleus and is essential for plant growth and development. In this study, a rice (Oryza sativa) mutant that exhibited albino and seedling-lethal phenotypes was isolated from a(60)Co-irradiated rice population. The mutant gene was identified as an ortholog of the Arabidopsis plastid transcriptionally active chromosome protein 2 (pTAC2) gene, and the mutant strain was designated osptac2. Sequence and transcription analyses showed that OspTAC2 encodes a putative chloroplast protein consisting of 10 pentratricopeptide repeat (PPR) domains and a C-terminal small MutS-related (SMR) domain...
September 15, 2016: Journal of Genetics and Genomics, Yi Chuan Xue Bao
Aneela Yasmeen, Sarfraz Kiani, Afshan Butt, Abdul Qayyum Rao, Faheem Akram, Aftab Ahmad, Idrees Ahmad Nasir, Tayyab Husnain, Shahid Mansoor, Imran Amin, Shaheen Aftab, Muhammad Zubair, Muhammad Nouman Tahir, Sohail Akhtar, Jodi Scheffler, Brian Scheffler
The conserved coat or V2 gene of begomoviruses is responsible for viral movement in the plant cells. RNAi technology was used to silence V2 gene for resistance against these viruses in transgenic plants. The transformation of the RNAi-based gene construct targeting V2 gene of CLCuKoV-Bur, cloned under 35S promoter, was done in two elite cotton varieties MNH-786 and VH-289 using shoot apex cut method of gene transformation. The transformation efficiency was found to be 3.75 and 2.88 % in MNH-786 and VH-289, respectively...
October 18, 2016: Molecular Biotechnology
Jinpeng Wang, Jiaxiang Yu, Pengchuan Sun, Yuxian Li, Ruiyan Xia, Yinzhe Liu, Xuelian Ma, Jigao Yu, Nanshan Yang, Tianyu Lei, Zhenyi Wang, Li Wang, Weina Ge, Xiaoming Song, Xiaojian Liu, Sangrong Sun, Tao Liu, Dianchuan Jin, Yuxin Pan, Xiyin Wang
Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ∼100 million years ago. There has been a standing controversy whether there had been five or seven basic chromosomes, before the tetraploidization, which were tackled but could not be well solved for the lacking of a sequenced and assembled outgroup plant to have a conservative genome structure. Recently, the availability of pineapple genome, which has not been subjected to the grass-common tetraploidization, provides a precious opportunity to solve the above controversy and to research into genome changes of rice and other grasses...
2016: Frontiers in Genetics
Shengfu Zhong, Lixia Ma, Syeda Akash Fatima, Jiezhi Yang, Wanquan Chen, Taiguo Liu, Yuting Hu, Qing Li, Jingwei Guo, Min Zhang, Li Lei, Xin Li, Shengwen Tang, Peigao Luo
The wheat powdery mildew resistance gene Pm40, which is located on chromosomal arm 7BS, is effective against nearly all prevalent races of Blumeria graminis f. sp tritici (Bgt) in China and is carried by the common wheat germplasm PI 672538. A set of the F1, F2 and F2:3 populations from the cross of the resistant PI 672538 with the susceptible line L1034 were used to conduct genetic analysis of powdery mildew resistance and construct a high-density linkage map of the Pm40 gene. We constructed a high-density linkage genetic map with a total length of 6...
2016: PloS One
Todd P Michael, Douglas Bryant, Ryan Gutierrez, Nikolai Borisjuk, Philomena Chu, Hanzhong Zhang, Jing Xia, Junfei Zhou, Hai Peng, Moaine El Baidouri, Boudewijn Ten Hallers, Alex R Hastie, Tiffany Liang, Kenneth Acosta, Sarah Gilbert, Connor McEntee, Scott A Jackson, Todd C Mockler, Weixiong Zhang, Eric Lam
Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Considering these biological features of Spirodela and its basal position in the monocot lineage, understanding its genome architecture could shed light on plant adaptation and genome evolution. Like many draft genomes, however, the 158 Mbp Spirodela genome sequence has not been resolved to chromosomes and important genome characteristics have not been defined. Here we deployed rapid genome-wide physical maps combined with high-coverage short-read sequencing to resolve the 20 chromosomes of Spirodela and to empirically delineate its genome features...
October 18, 2016: Plant Journal: for Cell and Molecular Biology
Billie A Gould, Yani Chen, David B Lowry
The early stages of speciation are often characterized by the formation of partially reproductively isolated ecotypes, which evolve as a byproduct of divergent selective forces that are endemic to different habitats. Identifying the genomic regions, genes, and ultimately functional polymorphisms that are involved in the processes of ecotype formation is inherently challenging, as there are likely to be many different loci involved in the process. To localize candidate regions of the genome contributing to ecotype formation, we conducted whole genome pooled-sequencing (pool-seq) with 47 coastal perennial and 50 inland annual populations of the yellow monkeyflower, Mimulus guttatus...
October 16, 2016: Molecular Ecology
Ying Liu, Lili Yu, Yue Qu, Jingjing Chen, Xiexiang Liu, Huilong Hong, Zhangxiong Liu, Ruzhen Chang, Matthew Gilliham, Lijuan Qiu, Rongxia Guan
Soil salinity reduces soybean growth and yield. The recently identified GmSALT3 (Glycine max salt Tolerance-associated gene on chromosome 3) has the potential to improve soybean yields in salinized conditions. Here we evaluate the impact of GmSALT3 on soybean performance under saline or non-saline conditions. Three sets of near isogenic lines (NILs), with genetic similarity of 95.6-99.3% between each pair of NIL-T and NIL-S, were generated from a cross between two varieties 85-140 (salt-sensitive, S) and Tiefeng 8 (salt-tolerant, T) by using marker-assisted selection...
2016: Frontiers in Plant Science
Angelica Giancaspro, Stefania L Giove, Daniela Zito, A Blanco, Agata Gadaleta
Fusarium head blight (scab) is one of the most widespread and damaging diseases of wheat, causing grain yield and quality losses and production of harmful mycotoxins. Development of resistant varieties is hampered by lack of effective resistance sources in the tetraploid wheat primary gene pool. Here we dissected the genetic basis of resistance in a new durum wheat (Triticum turgidum ssp. durum) Recombinant inbred lines (RILs) population obtained by crossing an hexaploid resistant line and a durum susceptible cultivar...
2016: Frontiers in Plant Science
A Rajeshwari, Barsha Roy, Natarajan Chandrasekaran, Amitava Mukherjee
The current study reveals the impact of gold nanorods (NRs) capped with CTAB (cetyltrimethylammonium bromide) or PEG (polyethylene glycol) on Allium cepa. The morphology and surface charge of CTAB- and PEG-capped gold NRs were characterized by electron microscopic and zeta potential analyses. The chromosomal aberrations like clumped chromosome, chromosomal break, chromosomal bridge, diagonal anaphase, disturbed metaphase, laggard chromosome, and sticky chromosome were observed in the root tip cells exposed to different concentrations (0...
October 6, 2016: Plant Physiology and Biochemistry: PPB
Jiafa Chen, Rosemary Shrestha, Junqiang Ding, Hongjian Zheng, Chunhua Mu, Jianyu Wu, George Mahuku
Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance...
October 14, 2016: G3: Genes—Genomes—Genetics
Kevin J Tsai, Mei-Yeh Jade Lu, Kai-Jung Yang, Mengyun Li, Yuchuan Teng, Shihmay Chen, Maurice S B Ku, Wen-Hsiung Li
The diploid C4 plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size. We have combined de novo assembly with custom reference-guided improvements on a popular cultivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents over 97% of the estimated 490 Mbp...
October 13, 2016: Scientific Reports
Mai Takagi, Takuya Sakamoto, Ritsuko Suzuki, Keiichirou Nemoto, Takeshi Obayashi, Takeshi Hirakawa, Tomoko M Matsunaga, Daisuke Kurihara, Yuko Nariai, Takeshi Urano, Tatsuya Sawasaki, Sachihiro Matsunaga
Aurora kinase (AUR) is a well-known mitotic serine/threonine kinase that regulates centromere formation, chromosome segregation, and cytokinesis in eukaryotes. In addition to regulating mitotic events, AUR has been shown to regulate protein dynamics during interphase in animal cells. In contrast, there has been no identification and characterization of substrates and/or interacting proteins during interphase in plants. The Arabidopsis thaliana genome encodes three AUR paralogues, AtAUR1, AtAUR2, and AtAUR3...
October 12, 2016: Journal of Plant Research
Corinna B Liller, Agatha Walla, Martin P Boer, Pete Hedley, Malcolm Macaulay, Sieglinde Effgen, Maria von Korff, G Wilma van Esse, Maarten Koornneef
Awn length was mapped using a multiparent population derived from cv. Morex and four wild accessions. One QTL was fine mapped and candidate genes were identified in NILs by RNA-seq. Barley awns are photosynthetically active and contribute to grain yield. Awn length is variable among both wild and cultivated barley genotypes and many mutants with alterations in awn length have been identified. Here, we used a multiparent mapping population derived from cv. Morex and four genetically diverse wild barley lines to detect quantitative trait loci (QTLs) for awn length...
October 12, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Hongju Jian, Kun Lu, Bo Yang, Tengyue Wang, Li Zhang, Aoxiang Zhang, Jia Wang, Liezhao Liu, Cunmin Qu, Jiana Li
Sucrose is the principal transported product of photosynthesis from source leaves to sink organs. SUTs/SUCs (sucrose transporters or sucrose carriers) and SWEETs (Sugars Will Eventually be Exported Transporters) play significant central roles in phloem loading and unloading. SUTs/SUCs and SWEETs are key players in sucrose translocation and are associated with crop yields. The SUT/SUC and SWEET genes have been characterized in several plant species, but a comprehensive analysis of these two gene families in oilseed rape has not yet been reported...
2016: Frontiers in Plant Science
Ana-Rosa Ballester, Yury Tikunov, Jos Molthoff, Silvana Grandillo, Marcela Viquez-Zamora, Ric de Vos, Ruud A de Maagd, Sjaak van Heusden, Arnaud G Bovy
Semi-polar metabolites such as flavonoids, phenolic acids, and alkaloids are very important health-related compounds in tomato. As a first step to identify genes responsible for the synthesis of semi-polar metabolites, quantitative trait loci (QTLs) that influence the semi-polar metabolite content in red-ripe tomato fruit were identified, by characterizing fruits of a population of introgression lines (ILs) derived from a cross between the cultivated tomato Solanum lycopersicum and the wild species Solanum chmielewskii...
2016: Frontiers in Plant Science
Chaoyang Zhou, Lingling Shi, Bin Ye, Haichao Feng, Ji Zhang, Ruifu Zhang, Xin Yan
Aside from applications in the production of commercial enzymes and metabolites, Bacillus amyloliquefaciens is also an important group of plant growth-promoting rhizobacteria that supports plant growth and suppresses phytopathogens. A host-genotype-independent counter-selectable marker would enable rapid genetic manipulation and metabolic engineering, accelerating the study of B. amyloliquefaciens and its development as both a microbial cell factory and plant growth-promoting rhizobacteria. Here, a host-genotype-independent counter-selectable marker pheS (*) was constructed through a point mutation of the gene pheS, which encodes the α-subunit of phenylalanyl-tRNA synthetase in Bacillus subtilis strain 168...
October 11, 2016: Applied Microbiology and Biotechnology
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