tThe thale cress Arabidopsis thaliana is a powerful model organism for studying a wide variety of biologicalprocesses. Recent advances in sequencing technology have resulted in a wealth of information describingnumerous aspects of A. thaliana genome function. However, there is a relative paucity of computationalsystems for efficiently and effectively using these data to create testable hypothes…
tThe Arabidopsis thaliana gynoecium arises at the center of the flower as a simple structure, which willsuccessively develop novel cell types and tissues, resulting in a complex organ. Genetic and hormonalfactors involved in this process have been identified, but we are still far from understanding how theseelements interact, and how these interactions rearrange according to spatial and tempora…
Shoots are ramifying systems with regular initiation of new growth axils called shoot branches. In seedplants, shoot buds initiate in leaf axils from axillary meristems (AMs) containing stem cells. The activitiesof AMs and buds play vital roles in plant architecture and crop yield. Whereas recent years have witnessedenormous progress the control of bud outgrowth, our knowledge of AM initiation …
Efficiently obtaining and utilizing energy and elements is critical for an organism to maximize its fitness.Optimizing these processes requires precise regulation and coordination of an organism’s metabolic net-works in response to diverse environmental conditions and developmental stages. Metabolic regulationis often considered to largely occur by allosteric feedback where the metabolites di…
Plants adapt to the prevailing photoperiod by adjustinggrowthandfloweringtotheavailabilityofenergy. To understand the molecul archanges involved in adaptation to along-dayconditionwecomprehensively profiled leaf six at the end of the day and theend of the night at four development al stages on Arabidopsis thaliana plants grownin a 16 hphotoperiod,andcompared the profilest othose from leaf 6of …
Marker assisted backcrossing (MABC) was used to transfer the three stem rust (Puccinia graminis tritici)resistant genes Sr25, SrWeb and Sr50 into the popular Indian wheat cv. HUW234. The donor was theCIMMYT breeding line PMBWIR4, and each of the target genes was marked by a simple PCR assay. Athree step screening strategy was adopted: the first screen comprised foreground selection, the secondu…
Insight into biological stress regulatory pathways can be derived from high-throughput transcriptomicdata using computational algorithms. These algorithms can be integrated into a computational approachto provide specific testable predictions that answer biological questions of interest. This review conceptu-ally organizes a wide variety of developed algorithms into a classification system base…
The information that connects genotypes and phenotypes is essentially embedded in research articleswritten in natural language. To facilitate access to this knowledge, we constructed a framework for thecuration of the scientific literature studying the molecular mechanisms that control leaf growth anddevelopment in Arabidopsis thaliana (Arabidopsis). Standard structured statements, called relat…
Grain protein content (GPC) in wheat has been a major trait of interest for breeders since it has enormousend use potential. In the present study, marker-assisted backcrossing (MABC) was successfully used toimprove GPC in wheat cultivar HUW468. The genotype Glu269 was used as the donor parent for intro-gression of the gene Gpc-B1 that confers high GPC. In a segregating population, SSR marker Xu…
Plant speciation and diversification strongly rely on structural changes in the nuclear genome, both at the whole ploidy and individual chromosome level. Phylogenetic, comparative mapping and cytological studies have provided insights into the evolutionary mechanisms that shape the plant genome. These include major genome alterations, such as whole genome duplication and hybridization (auto- an…
Retrotransposons are major components of higher plant genomes, and long terminal repeat (LTR) retro-transposons are especially predominant. Thus, numerous LTR retrotransposon families with high copynumbers exist in most plant genomes. As the integrated copies of these retrotransposons are geneticallyinherited, their insertion polymorphisms among crop cultivars have been used as functional molec…
Recent access to Triticeae genome sequences as well as high resolution gene-based genetic maps recentlyoffered the opportunity to compare modern Triticeae genomes and model their evolutionary history fromtheir reconstructed founder ancestors. In silico paleogenomic data have revealed the evolutionary forcesthat have shaped present-day Triticeae and allowed to gain insight into how wheat, barley…
tTransfer of mitochondrial genes to the nucleus, and subsequent gain of regulatory elements for expres-sion, is an ongoing evolutionary process in plants. Many examples have been characterized, which insome cases have revealed sources of mitochondrial targeting sequences and cis-regulatory elements. Incontrast, there have been no reports of a nuclear gene that has undergone intracellular transf…
tC4photosynthesis is a trait that has evolved in 66 independent plant lineages and increases the efficiencyof carbon fixation. The shift from C3to C4photosynthesis requires substantial changes to genes andgene functions effecting phenotypic, physiological and enzymatic changes. We investigate the role ofancient whole genome duplications (WGD) as a source of new genes in the development of this …
tAccurate annotation of protein function is key to understanding life at the molecular level, but auto-mated annotation of functions is challenging. We here demonstrate the combination of a method forprotein function annotation that uses network information to predict the biological processes a proteinis involved in, with a sequence-based prediction method. The combined function prediction is b…
The sunflower (Helianthus annuus) and species belonging to the genus Helianthus are emerging as amodel species and genus for a number of studies on genome evolution. In this review, we report on therepetitive component of the H. annuus genome at the biochemical, molecular, cytological, and genomiclevels. Recent work on sunflower genome composition is described, with emphasis on different typeso…
Rice bean (Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular…
To enhance the yield potential of an elite indica rice cultivar, an introgression (BC3-derived) line of IR64, YTH288, was developed using a new-plant-type cultivar,IR66215-44-2-3, as a donor parent. YTH288 has agronomically valuable characteristics such as large panicles, few unproductive tillers, and large leaves inherited from NPT. To identify the genetic basis of these traits, we used 167 F…
Clustering genotype × environment (GE) interactions and understanding the causes of GE interactions are among the most important tasks in crop breeding programs. Pattern analysis (cluster and ordination techniques) was applied to analyze GE interactions for grain yield of 24 durum wheat (Triticum turgidum L. var. durum) genotypes (breeding lines and old and new cultivars) along with a popular …
The purpose of this studywas to investigate the physiological responses of drought-tolerant and drought-susceptible soybean genotypes to exogenous abscisic acid (ABA) application during progressive soil drying at seedling stages. Five-day old soybean seedlings were transplanted into PVC tubes filledwith soilmixture. Seedlingswerewatered dailywith similarwater volumes until second trifoliate lea…
The present experiment was conducted to evaluate the effect of elevated [CO2] with varying nutrient management on rice–rice production system. The experiment was conducted in the open field and inside open-top chambers (OTCs) of ambient [CO2] (≈390 μmol L−1) and elevated [CO2] environment (25% above ambient) during wet and dry seasons in 2011–2013 at Kharagpur, India. The nutrient man…
Powdery mildew, caused by Erysiphe pisi D.C., is a major constraint to pea production worldwide. The pea cultivar Xucai 1 has shown high resistance to E. pisi under greenhouse and field conditions. The objectives of this study were to identify and characterize genes conferring resistance to powdery mildew in Xucai 1. Three crosses, Qizhen 76 × Xucai 1, Bawan 6 × Xucai 1, and Xucai 1 × Bawan…
Barnyard millet (Echinochloa spp.) is one of the most underresearched crops with respect to characterization of genetic resources and genetic enhancement. A total of 95 germplasm lines representing global collection were evaluated in two rainy seasons at Almora,Uttarakhand, India for qualitative and quantitative traits and the data were subjected to multivariate analysis. High variation was ob…
Seed aging decreases the quality and vigor of crop seeds, thereby causing substantial agricultural and economic losses in crops. To identify genetic differences in seed aging between homozygotes and heterozygotes in maize, the seeds of a set of recombinant inbred lines (RILs) and an immortalized F2 (IF2) population were subjected to artificial aging treatments for 0, 2, 3, and 4 days under 45 �…
We investigated genetic variation of a rice HEADING DATE 1(HD1) homolog in foxtail millet. First, we searched for a rice HD1 homolog in a foxtail millet genome sequence and designed primers to amplify the entire coding sequence of the gene. We compared full HD1 gene sequences of 11 accessions (including Yugu 1, a Chinese cultivar used for genome sequencing) from various regions in Europe and A…
A two-year field experiment (2012–2013) was conducted to investigate the effects of two tillage methods and five maize straw mulching patterns on the yield, water consumption,and water use efficiency (WUE) of spring maize (Zea mays L.) in the northern Huang–Huai–Hai valley of China. Compared to rotary tillage, subsoil tillage resulted in decreases in water consumption by 6.3–7.8% and i…
Plants have evolved sophisticated defensemechanisms against herbivores to help them adapt to the environment. Understanding the defense mechanisms in plants can help us control insects in a more effective manner. In this study, we found that compared with Tianlong 2 (a cultivated soybean with insect susceptibility), ED059 (a wild soybean line with insect resistance) contains sharper pubescence …
The ameliorative effect of fulvic acid (0, 300, and 600 mg L−1) on photosystem II and antioxidant enzyme activity of the rapeseed (Brassica napus L.) plant under water stress (60, 100, and 140 mm evaporation from class A pan) was studied using split plots in a randomized complete block design with three replications. Results indicated that application of fulvic acid (FA) improved the maximum…
Stem growth habit is an important agronomic trait in soybean and is subject to artificial selection. This study aimed to provide a theory for genotypic selection of stem growth habit for breeding purposes by analyzing the alleles of GmTfl1 gene in Chinese soybean varieties and establishing a database of GmTfl1 variation. Using knowledge of insertion and deletion (Indel) in the non-coding regio…
The rich genetic variation preserved in collections of Aegilops tauschii can be readily exploited to improve common wheat using synthetic hexaploid wheat lines. However,hybrid necrosis, which is characterized by progressive death of leaves or plants, has been observed in certain interspecific crosses between tetraploid wheat and Ae. tauschii. The aim of this study was to construct a fine geneti…
Understanding functional relations among plant traits and their modulation by growing conditions is imperative in designing selection strategies for breeding programs. This study assessed trait relationships among 196 common bean genotypes exposed to stresses for drought and field infestation of bean fly or bean stem maggot (BSM). The study was carried out at two locations and data was analyzed…
Plants may respond to drought by altering biomass allocation to shoots and roots or by changing the metabolic activities in these organs. To determine how drought changes the partitioning of carbon allocated to growth and secondary metabolism in maize roots and how it affects photosynthesis (A) and productivity in maize, we evaluated leaf gas exchange, yield componentes, root morphology, and pr…
Soil phosphorus (P) fractionation, adsorption, and desorption isotherm, and rice yield and P uptakewere investigated in flooded tropical rice (Oryza sativa L.) following 42-year fertilizer and manure application. The treatments included low-input [unfertilized control without N, P, or K (C0N0)], farmyard manure (FYM) (C1N0), NP (C0NP), NPK (C0NPK), FYM + NP (C1NP), and high-input treatment, FYM…
Differences in soil physical, chemical and biological properties between paddy–upland and continuous upland rotations will influence nutrient relations and crop growth. With the aim of estimating rapeseed yield performance in response to fertilization in rice–rapeseed (RR) and cotton–rapeseed (CR) rotations, on-farm experiments were conducted at 70 sites across Hubei province, central Chi…
Aegilops tauschii Ais a wild relative of commonwheat (Triticum aestivum) and acts as an important resource of elite genes including genes for resistance to biotic and abiotic stresses. To improve the cadmium(Cd) tolerance ofwheat varieties using A. tauschii resources, we investigated the genetic variation of biomass-based Cd tolerance in 235 A. tauschii accessions treated with 0 (control) and 1…
Biotic and abiotic stresses are major limiting factors for high crop productivity worldwide. A landrace collection consisting of 380 durum wheat (Triticum turgidum L. var. durum) entries originating in several countries alongwith four check varieties were evaluated for biotic stresses:yellow rust (Puccinia striiformis Westendorf f. sp. tritici) andwheat stemsawfly (WSS) Cephus cinctus Norton (H…
The objective of this study was to evaluate the effects of wheat variety, food processing, and milling method on antioxidant properties. Black wheat variety Heibaoshi 1 had the highest total phenolic content (659.8 μg gallic acid equivalents g−1), total flavonoid content (319.3 μg rutin equivalents g−1), and antioxidant activity, whereas light purple wheat variety Shandongzimai 1 had the …
Plant water use efficiency (WUE) is becoming a key issue in semiarid areas, where crop production relies on the use of large volumes of water. Improving WUE is necessary for securing environmental sustainability of food production in these areas. Given that climate change predictions include increases in temperature and drought in semiarid regions, improving crop WUE is mandatory for global foo…
Intensification in rice crop production is generally understood as requiring increased use of material inputs: water, inorganic fertilizers, and agrochemicals. However, this is not the only kind of intensification available. More productive crop phenotypes, with traits such as more resistance to biotic and abiotic stresses and shorter crop cycles, are possible through modifications in the manag…
While the yield potential of rice has increased but little is known about the impact of breeding on grain quality, especially under different levels of N availability. In order to investigate the integrated effects of breeding andNlevels on rice quality 12 japonica rice cultivars bred in the past 60 years in the Yangtze River Basinwere usedwith three levels of N: 0 kg N ha−1, 240 kg N ha−1,…
Rice (Oryza sativa L.) is one of the most important staple crops in China. Increasing atmospheric greenhouse gas concentrations and associated climate change may greatly affect rice production. We assessed the potential impacts of climate change on cold rice production in the Heilongjiang province, one of China's most important rice production regions. Data for a baseline period (1961–1990) a…
Field pea (Pisum sativum L.) is an important protein-rich pulse crop produced globally. Increasing the lipid content of Pisum seeds through conventional and contemporary molecular breeding tools may bring added value to the crop. However, knowledge about genetic diversity and lipid content in field pea is limited. An understanding of genetic diversity and population structure in diverse germpla…
Allene oxide cyclase (AOC, E 5.3.99.6) is an essential enzyme in the jasmonic acid (JA)biosynthetic pathway and mediates a wide range of adaptive responses. In this report, five AOC genes (GhAOC1–GhAOC5) were cloned from upland cotton (Gossypium hirsutum L.),sequenced, and characterized. Real-time PCR analysis indicated that the transcripts of GhAOCs were abundantly expressed in roots and le…
The colonization of maize (Zea mays L.) and peanut (Arachis hypogaea L.) by the fungal pathogen Aspergillus flavus results in the contamination of kernels with carcinogenic mycotoxins known as aflatoxins leading to economic losses and potential health threats to humans. The regulation of aflatoxin biosynthesis in various Aspergillus spp. has been extensively studied, and has been shown to be r…
The biotrophic fungus Puccinia striiformis f. sp. tritici is the causal agent of the yellow rust in wheat. Between the years 2010–2013 a new strain of this pathogen (Warrior/Ambition),against which the present cultivated wheat varieties have no resistance, appeared and spread rapidly. It threatens cereal production in most of Europe. The search for sources of resistance to this strain is prop…
Plant phenomics has the potential to accelerate progress in understanding gene functions and environmental responses. Progress has been made in automating high-throughput plant phenotyping. However, few studies have investigated automated rice panicle counting. This paper describes a novel method for automatically and nonintrusively determining rice panicle numbers during the full heading stage…
EST sequences of Mentha piperita available in the public domain (NCBI) were exploited to develop SSR markers. A total of 1316 ESTs were assembled into 155 contigs and 653 singletons and of these, 110 sequences were found to contain 130 SSRs, with a frequency of 1 SSR/3.4 kb. Dinucleotide repeat SSRs were most frequent (72.3%) with the AG/CT (43.8%) repeat motif followed by AT/AT (16.2%). Primer…
Conventional flat planting is commonly used for growing wheat in Pakistan and the crop is irrigated by flood irrigation, but it leads to ineffective use of applied nitrogen owing to poor aeration and leaching and volatilization losses. The practice also results in greater crop lodging, lower water use efficiency, and crusting of the soil surface. In contrast, bed planting of wheat not only save…
QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in biparental populations. Eight functionalities are integrated in this software package: (1) BIN: binning of redundant markers;(2) MAP: construction of linkage maps in biparental populations; (3) CMP: consensus map construction from multiple linkage maps sh…
This research aims to determine the range of parameter value, baseflow index and the appropriate method for base flow separation. Seven (7) recursive-digital-filters (RDF) and two (2) graphical methods are used for this study. Discharge data from 8 watersheds in the administrative area of UPT PSDA Bondowoso in East Java were used to test the methods. Firstly, each method was calibrated using…