Heat Stress Tolerance in Rice (Oryza sativa L.): Identification of Quantitative Trait Loci and Candidate Genes for Seedling Growth Under Heat Stress

Productivity of rice, world's most important cereal is threatened by high temperature stress, intensified by climate change. Development of heat stress-tolerant varieties is one of the best strategies to maintain its productivity. However, heat stress tolerance is a multigenic trait and the candidate genes are poorly known. Therefore, we aimed to identify quantitative trait loci (QTL) for vegetative stage tolerance to heat stress in rice and the corresponding candidate genes. We used genotyping-by-sequencing to generate single nucleotide polymorphic (SNP) markers and genotype 150 F8 recombinant inbred lines (RILs) obtained by crossing heat tolerant “N22” and heat susceptible “IR64” varieties. A linkage map was constructed using 4,074 high quality SNP markers that corresponded to 1,638 recombinationally unique events in this mapping population. Six QTL for root length and two for shoot length under control conditions with 2.1–12% effect were identified. One QTL rlht5.1 was identified for “root length under heat stress,” with 20.4% effect. Four QTL were identified for “root length under heat stress as percent of control” that explained the total phenotypic variation from 5.2 to 8.6%. Three QTL with 5.3–10.2% effect were identified for “shoot length under heat stress,” and seven QTL with 6.6–19% effect were identified for “shoot length under heat stress expressed as percentage of control.” Among the QTL identified six were overlapping between those identified using shoot traits and root traits: two were overlapping between QTL identified for “shoot length under heat stress” and “root length expressed as percentage of control” and two QTL for “shoot length as percentage of control” were overlapping a QTL each for “root length as percentage of control” and “shoot length under heat stress.” Genes coding 1,037 potential transcripts were identified based on their location in 10 QTL regions for vegetative stage heat stress tolerance. Among these, 213 transcript annotations were reported to be connected to stress tolerance in previous research in the literature. These putative candidate genes included transcription factors, chaperone proteins (e.g., alpha-crystallin family heat shock protein 20 and DNAJ homolog heat shock protein), proteases, protein kinases, phospholipases, and proteins related to disease resistance and defense and several novel proteins currently annotated as expressed and hypothetical proteins

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Identification of QTLs associated with root architectural pattern during domestication of common bean (Phaseolus vulgaris L.)

Domestication of crop plants involves the selection for the most desirable phenotypes, and results in the alteration of allele frequencies of certain target loci. Previous analyses of domestication have mainly focused on above-ground plant organs, while root traits have been largely neglected mainly due to the visual inaccessibility of this organ. However, it is very likely that some domestication-associated changes in root growth and architecture might have happened as a consequence of selection for above-ground plant parts as these organs operate in functional equilibrium with each other. Thus, we hypothesized that domestication of the common bean brought about changes in root traits controlled by two types of genes, one that controls root growth only, while the other regulates the functional balance between root and shoot. We have performed a QTL analysis using a recombinant inbred population derived from a cross between a landrace (G19833) and a wild accession (G23419), both from the Andean gene pool. A SNP-based linkage map was constructed using the genotyping-by-sequencing (GBS) approach. Time series root images were collected using a novel 2-dimensional phenotyping platform. Phenotypic and genotyping information was used to identify various root and shoot related QTLs. Like previous domestication studies, QTLs for different traits were clustered on various genomic regions

Potential role of weather, soil and plant microbial communities in rapid decline of apple trees.

An unusual decline and collapse of young established trees known as "rapid apple decline" (RAD) has become a major concern for apple growers, particularly in the northeastern United States. This decline is characterized by stunted growth, pale yellow to reddish leaves, and tree collapse within weeks after onset of symptoms. We studied declining apple trees to identify potential involvement of abiotic and biotic stresses. We used 16S and ITS to profile bacterial and fungal communities in the soil, rhizosphere, roots, and shoots and tested for the presence of six viruses in scions and rootstocks of symptomatic and asymptomatic trees. The viruses detected were not associated with RAD symptoms. Bacterial and fungal populations were highly variable in plant tissue, soil and rhizosphere samples, with bacteroidetes, firmicutes, proteobacteria, acidobacteria, and actinobacteria the predominant bacterial classes in various samples. 'Alphaproteobacteria-rickettsiales', a bacterial class usually reduced in water-limiting soils, had significantly low abundance in root samples of symptomatic trees. Basidiomycota and Ascomycota fungal classes were the most common fungal classes observed, but neither showed differential enrichment between symptomatic and asymptomatic trees. Analyzing weather data showed an extremely cold winter followed by drought in 2015-2016, which likely weakened the trees to make them more susceptible to varied stresses. In addition, similar physical and nutritional soil composition from symptomatic and asymptomatic trees rules out the role of nutritional stress in RAD. Necrotic lesions and wood decay symptoms dispersing from bark or vascular cambium towards the heartwood were observed primarily below the graft union of declining apple trees, suggesting that the rootstock is the originating point of RAD. We speculate that differences in abiotic factors such as moisture levels in declining roots in combination with extreme weather profiles might cause RAD but cannot clearly rule out the involvement of other factors

Dynamic transcriptome profiling of Bean Common Mosaic Virus (BCMV) infection in Common Bean (Phaseolus vulgaris L.)

Background Bean common mosaic virus (BCMV) is widespread, with Phaseolus species as the primary host plants. Numerous BCMV strains have been identified on the basis of a panel of bean varieties that distinguish the pathogenicity types with respect to the viral strains. The molecular responses in Phaseolus to BCMV infection have not yet been well characterized. Results We report the transcriptional responses of a widely susceptible variety of common bean (Phaseolus vulgaris L., cultivar ‘Stringless green refugee’) to two BCMV strains, in a time-course experiment. We also report the genome sequence of a previously unreported BCMV strain. The interaction with the known strain NL1-Iowa causes moderate symptoms and large transcriptional responses, and the newly identified strain (Strain 2 or S2) causes severe symptoms and moderate transcriptional responses. The transcriptional profiles of host plants infected with the two isolates are distinct, and involve numerous differences in splice forms in particular genes, and pathway specific expression patterns. Conclusions We identified differential host transcriptome response after infection of two different strains of Bean common mosaic virus (BCMV) in common bean (Phaseolus vulgaris L.). Virus infection initiated a suite of changes in gene expression level and patterns in the host plants. Pathways related to defense, gene regulation, metabolic processes, photosynthesis were specifically altered after virus infection. Results presented in this study can increase the understanding of host-pathogen interactions and provide resources for further investigations of the biological mechanisms in BCMV infection and defense.This article is published as Martin, Kathleen, Jugpreet Singh, John H. Hill, Steven A. Whitham, and Steven B. Cannon. "Dynamic transcriptome profiling of Bean Common Mosaic Virus (BCMV) infection in Common Bean (Phaseolus vulgaris L.)." BMC genomics 17, no. 1 (2016): 613. doi: 10.1186/s12864-016-2976-8. Posted with permission.</p

Differential gene regulatory pathways and co-expression networks associated with fire blight infection in apple (Malus × domestica)

Disease resistance: How apples fight blight Different apple varieties, such as ‘Gala’ and ‘Empire,’ defend themselves against fire blight in different ways, and studying how they do it may help in breeding varieties with better resistance. Fire blight is a devastating bacterial disease that can destroy entire orchard blocks in a single season. Breeding for increased resistance is one of the most efficient ways to combat it. Some apple varieties are naturally more resistant than others, but the underlying genetics are not well understood. Awais Khan at Cornell University in New York and co-workers investigated how the ‘Gala’ and ‘Empire’ varieties defend themselves in the first 72 h after infection. ‘Empire’ showed stronger resistance than ‘Gala,’ with many distinct resistance mechanisms. The researchers identified several resistance genes in each variety, which may eventually be used in breeding more blight-resistant apple varieties

A transcriptome‑SNP‑derived linkage map of \u3ci\u3eApios americana\u3c/i\u3e (potato bean) provides insights about genome re‑organization and synteny conservation in the phaseoloid legumes

Apios (Apios americana; “apios”), a tuberous perennial legume in the Phaseoleae tribe, was widely used as a food by Native Americans. Work in the last 40 years has led to several improved breeding lines. Aspects of the pollination biology (complex floral structure and tripping mechanism) have made controlled crosses difficult, and the previous reports indicated that the plant is likely primarily an outcrosser. We used a pseudo-testcross strategy to construct a genetic map specific to the maternal parent. The map was built using single-nucleotide polymorphism markers identified by comparing the expressed sequences of individuals in the mapping population against a de novo maternal reference transcriptome assembly. The apios map consists of 11 linkage groups and 1121 recombinationally distinct loci, covering ~ 938.6 cM. By sequencing the transcriptomes of all potential pollen parents, we were able to identify the probable pollen donors and to discover new aspects of the pollination biology in apios. No selfing was observed, but multiple pollen parents were seen within individual pods. Comparisons with genome sequences in other species in the Phaseoleae showed extended synteny for most apios linkage groups. This synteny supports the robustness of the map, and also sheds light on the history of the Phaseoleae, as apios is relatively early diverging in this tribe. We detected a translocation event that separates apios and two Vigna species from Phaseolus vulgaris and Glycine max. This apios mapping work provides a general protocol for sequencing-based construction of high-density linkage maps in outcrossing species with heterogeneous pollen parents

Dynamic transcriptome profiling of Bean Common Mosaic Virus (BCMV) infection in Common Bean (Phaseolus vulgaris L.)

Background Bean common mosaic virus (BCMV) is widespread, with Phaseolus species as the primary host plants. Numerous BCMV strains have been identified on the basis of a panel of bean varieties that distinguish the pathogenicity types with respect to the viral strains. The molecular responses in Phaseolus to BCMV infection have not yet been well characterized. Results We report the transcriptional responses of a widely susceptible variety of common bean (Phaseolus vulgaris L., cultivar ‘Stringless green refugee’) to two BCMV strains, in a time-course experiment. We also report the genome sequence of a previously unreported BCMV strain. The interaction with the known strain NL1-Iowa causes moderate symptoms and large transcriptional responses, and the newly identified strain (Strain 2 or S2) causes severe symptoms and moderate transcriptional responses. The transcriptional profiles of host plants infected with the two isolates are distinct, and involve numerous differences in splice forms in particular genes, and pathway specific expression patterns. Conclusions We identified differential host transcriptome response after infection of two different strains of Bean common mosaic virus (BCMV) in common bean (Phaseolus vulgaris L.). Virus infection initiated a suite of changes in gene expression level and patterns in the host plants. Pathways related to defense, gene regulation, metabolic processes, photosynthesis were specifically altered after virus infection. Results presented in this study can increase the understanding of host-pathogen interactions and provide resources for further investigations of the biological mechanisms in BCMV infection and defense

Pseudostellaria heterantha Pax

原著和名: ワチガヒサウ科名: ナデシコ科 = Caryophyllaceae採集地: 茨城県 筑波山 (常陸 筑波山)採集日:採集者: 萩庭丈壽整理番号: JH008572国立科学博物館整理番号: TNS-VS-95857

Wild melon diversity in India (Punjab State)

We present here the first comprehensive genetic characterization of wild melon accessions from northern India. The genetic diversity among 43 wild melon accessions collected from the six agro-ecological regions of the Punjab State of India was assessed by measuring variation at 16 Simple Sequence Repeat (SSR) loci, morphological traits of plant habit and fruit morphological traits, two yield-associated traits, root nematode resistance and biochemical composition (ascorbic acid, carotenoids, titrable acidity). Variation among accessions was observed in plant habit and fruit traits and wild melon germplasm with high acidity and elevated carotenoid content and possessing resistance to was identified in the collection. A high level of genetic variability in wild melon germplasm was suggested by SSR analysis. Comparative analysis using SSRs of the genetic variability between wild melons from the north and other melons from the south and east regions of India and also reference accessions of cultivated melon from Spain, Japan, Korea, Maldives, Iraq and Israel, showed regional differentiation among Indian melon accessions and that Indian germplasm was not closely related to melon accessions from other parts of the world. A highly drought tolerant accession belonging to var. Naud. was also identified.Anamika Roy was supported by a Fellowship from the Indian Council of Agricultural Research (ICAR). N.P.S. Dhillon was supported by a fellowship for sabbatical stays from the Spanish Ministerio de Ciencia e Innovacion, which also funded the research under grants AGL2006-12780-C02-01 and AGL2009-12698-C02-02. We are thankful to numerous students of Punjab Agricultural University for providing help during germplasm collection work and Fuensanta Garcia for technical support. We are grateful to Dr. James D. McCreight and Dr. G.J. Jellis for helpful comments.Roy, A.; Bal, SS.; Fergany, M.; Kaur, S.; Singh, H.; Malik, AA.; Singh, J.... (2012). Wild melon diversity in India (Punjab State). Genetic Resources and Crop Evolution. 59(5):755-767. https://doi.org/10.1007/s10722-011-9716-3S755767595Bajaj LK, Kaur G (1981) Spectrophotometric determination of l-ascorbic acid in vegetables and fruits. Analyst 106:17–120Dhillon NPS, Ranjana R, Singh K, Eduardo I, Monforte AJ, Pitrat M, Dhillon NK, Singh PP (2007) Diversity among landraces of Indian snapmelon (Cucumis melo var. momordica). Genet Resour Crop Evol 54:1267–1283Dhillon NPS, Singh J, Fergany M, Monforte AJ, Sureja AK (2009) Phenotypic and molecular diversity among landraces of snapmelon (Cucumis melo var. momordica) adapted to the hot and humid tropics of eastern India. Plant Genet Resour Charact Util 7:291–300Doyle JJ, Doyle JL (1990) Isolation of DNA from fresh tissue. Focus 12:13–15Fergany M, Kaur B, Monforte AJ, Pitrat M, Rys C, Lecoq H, Dhillon NPS, Dhaliwal SS (2011) Variation in melon (Cucumis melo) landraces adapted to the humid tropics of southeren India. Genet Resour Crop Evol 58:225–243Fernandez-Silva I, Eduardo I, Blanca J, Esteras C, Picó B, Nuez F, Arús P, Garcia-Mas J, Monforte AJ (2008) Bin mapping of genomic and EST-derived SSRs in melon (Cucumis melo L.). Theor Appl Genet 118:139–150Garcia-Mas J, Oliver M, Gomez-Paniagua H, DeVicente MC (2000) Comparing AFLP, RAPD and RFLP markers for measuring genetic diversity in melon. Theor Appl Genet 101:860–864Granberry DM, Norton JD (1980) Response of progeny from interspecific cross of Cucumis melo × C. metuliferus to Meloidogyne incognita acrita. J Am Soc Hortic Sci 105:180–183Jeffrey C (1980) A review of the Cucurbitaceae. Bot J Linn Soc 81:233–247Jeffrey C (2001) Cucurbitaceae. In: Hanelt P, Institute of Plant Genetics and Crop Plant Research (eds) Mansfeld’s encyclopedia of agricultural and horticultural crops. Springer, Heidelberg-New York, pp 1510–1557Kirkbride JH (1993) Biosystemetic monograph of the genus Cucumis (Cucurbitaceae): botanical identification of cucumbers and melons. Parkway, Boone, NCLiu K, Muse SV (2005) Powermaker: integrated analysis environment for genetic marker data. Bioinformatics 21:2128–2129Luan F, Delannay I, Staub JE (2008) Chinese melon (Cucumis melo L.) diversity analyses provide strategies for germplasm curation, genetic improvement, and evidentiary support of domestication patterns. Euphytica 164:445–461Monforte AJ, Garcia-Mas J, Arus P (2003) Genetic variability in melon based on microsatellite variation. Plant Breed 122:153–157Monforte AJ, Eduardo I, Abad S, Arus P (2005) Inheritance mode of fruit traits in melon-heterosis for fruit shape and its correlation with genetic distance. Euphytica 144:31–38Morri S, Fujishita N, Momodani Y (1980) Phylogenetic analysis in C. melo based on isozyme polymorphism, with special reference to the relationship between weed melon and cultivated melon. J Jpn Soc Hortic Sci 49:188–189Munger HM, Robinson RW (1991) Nomenclature of Cucumis melo L. Cucurbit Genet Coop 14:43–44Nallathambi P, Umamaheswari C, Samadia DK (2002) Arid cucrbit germplasm as potential source of disease resistance. In: Proceedings international conference on vegetables, November 11–14, 2002, Bangaloree, India, p 20Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J Mol Evol 19:153–170Pandey A, Tomer AK, Bhandari DC, Pareek SK (2008) Towards collection of wild relatives of crop plants in India. Genet Resour Crop Evol 55:187–202Pareek OP, Samadia DK (2002) Promising indigenous cucurbit varieties. Indian Hortic 47:15–18Pitrat M, Hanelt P, Hammer K (2000) Some comments on infraspecific classification of cultivars of melon. Acta Hortic 510:29–36Sebastian P, Schaefer H, Telford IRH, Renner SS (2010) Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia. Proc Natl Acad Sci USA 107:14269–14273Sehgal JL, Mandal DK, Mandal C, Vadivelu S (1992) Agroecological regions of India. National Bureau of Soil Survey and Land use Planning (ICAR), Nagpur, IndiaStepansky A, Kovalski I, Perl-Treves R (1999) Intraspecific classification of melons (Cucumis melo L.) in view of their phenotypic and molecular variation. Plant Syst Evol 217:313–332Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599Taylor AL, Droplan VH, Martin GC (1955) Perineal pattern of root knot nematodes. Phytopathology 45:26–34Thomas P, Joshi MR (1977) Total carotenoids. Potato Res 20:7