Linkage QTL Mapping and Genome-Wide Association Study on Resistance in Chickpea to Pythium ultimum

The soilborne oomycete plant pathogen Pythium ultimum causes seed rot and pre-emergence damping-off of chickpea (Cicer arietinum L.). The pathogen has been controlled for several decades using the fungicide metalaxyl as seed treatment but has re-emerged as a severe problem with the detection of metalaxyl-resistant isolates of the pathogen from infested fields in the United States Pacific Northwest. The objective of this study was to identify genetic markers and candidate genes associated with resistance to P. ultimum in an interspecific recombinant inbred line population (CRIL-7) derived from a cross between C. reticulatum (PI 599072) x C. arietinum (FLIP 84-92C) and conduct genome-wide association studies (GWAS) for disease resistance using a chickpea diversity panel consisting of 184 accessions. CRIL-7 was examined using 1029 SNP markers spanning eight linkage groups. A major QTL, “qpsd4-1,” was detected on LG 4 that explained 41.8% of phenotypic variance, and a minor QTL, “qpsd8-1,” was detected on LG8 that explained 4.5% of phenotypic variance. Seven candidate genes were also detected using composite interval mapping including several genes previously associated with disease resistance in other crop species. A total of 302,902 single nucleotide polymorphic (SNP) markers were used to determine population structure and kinship of the diversity panel. Marker–trait associations were established by employing different combinations of principal components (PC) and kinships (K) in the FarmCPU model. Genome-wide association studies detected 11 significant SNPs and seven candidate genes associated with disease resistance. SNP Ca4_1765418, detected by GWAS on chromosome 4, was located within QTL qpsd4-1 that was revealed in the interspecific CRIL-7 population. The present study provides tools to enable MAS for resistance to P. ultimum and identified genomic domains and candidate genes involved in the resistance of chickpea to soilborne diseases

Prediction of mitochondrial proteins of malaria parasite using split amino acid composition and PSSM profile

The rate of human death due to malaria is increasing day-by-day. Thus the malaria causing parasite Plasmodium falciparum (PF) remains the cause of concern. With the wealth of data now available, it is imperative to understand protein localization in order to gain deeper insight into their functional roles. In this manuscript, an attempt has been made to develop prediction method for the localization of mitochondrial proteins. In this study, we describe a method for predicting mitochondrial proteins of malaria parasite using machine-learning technique. All models were trained and tested on 175 proteins (40 mitochondrial and 135 non-mitochondrial proteins) and evaluated using five-fold cross validation. We developed a Support Vector Machine (SVM) model for predicting mitochondrial proteins of P. falciparum, using amino acids and dipeptides composition and achieved maximum MCC 0.38 and 0.51, respectively. In this study, split amino acid composition (SAAC) is used where composition of N-termini, C-termini, and rest of protein is computed separately. The performance of SVM model improved significantly from MCC 0.38 to 0.73 when SAAC instead of simple amino acid composition was used as input. In addition, SVM model has been developed using composition of PSSM profile with MCC 0.75 and accuracy 91.38%. We achieved maximum MCC 0.81 with accuracy 92% using a hybrid model, which combines PSSM profile and SAAC. When evaluated on an independent dataset our method performs better than existing methods. A web server PFMpred has been developed for predicting mitochondrial proteins of malaria parasites (http://www.imtech.res.in/raghava/pfmpred/)

HaptenDB: a comprehensive database of haptens, carrier proteins and anti-hapten antibodies

The key requirement for successful immunochemical assay is the availability of antibodies with high specificity and desired affinity. Small molecules, when used as haptens, are not immunogenic. However, on conjugating with carrier molecule they elicit antibody response. The production of anti-hapten antibodies of desired specificity largely depends on the hapten design (preserving greatly the chemical structure and spatial conformation of target compound), selection of the appropriate carrier protein and the conjugation method. This manuscript describes a curated database HaptenDB, where information is collected from published literature and web resources. The current version of the database has 2021 entries for 1087 haptens and 25 carrier proteins, where each entry provides comprehensive details about (1) nature of the hapten, (2) 2D and 3D structures of haptens, (3) carrier proteins, (4) coupling method, (5) method of anti-hapten antibody production, (6) assay method (used for characterization) and (7) specificities of antibodies. The current version of HaptenDB covers a wide array of haptens including pesticides, herbicides, insecticides, drugs, vitamins, steroids, hormones, toxins, dyes, explosives, etc. It provides internal and external links to various databases/resources to obtain further information about the nature of haptens, carriers and respective antibodies. For structure similarity comparison of haptens, the database also integrates tools like JME Editor and JMOL for sketching, displaying and manipulating hapten 2D/3D structures online. So the database would be of great help in identifying functional group(s) in smaller molecules using antibodies as well as for the development of immunodiagnostics/therapeutics by providing data and procedures available so far for the generation of specific or cross-reactive antibodies. Availability: HaptenDB is available on http://www.imtech.res.in/raghava/haptendb/ and http://bioinformatics.uams.edu/raghava/haptendb/ (Mirror site)

Legume seed production for sustainable seed supply and crop productivity: case of groundnut in Tanzania and Uganda

Improvingagriculturalproductivityandproductionisaprerequisite to sustain rural livelihoods in developing countries of sub-Saharan Africa SSA).Thisrequiresincreaseduseofqualityseedofimproved and well-adapted crop varieties. Legumes are particularly critical in ensuring food and nutritional securities of the majority of farming households. However, their productivity has been constrained because of limited availability of quality seed, jeopardizing henceforth food security and rural livelihoods. The lack of interest in productionoflegumeseedsbypotentialseedproducers,especially the private sector, is attributable to limited information on the cost and profitability of producing these seeds. Using primary data collectedfromTanzaniaandUganda,weanalyzedthecoststructureof improved groundnut (Arachis hypogaea L.) seed production to assess viability. We adopted cost-benefit analysis framework to evaluate different seed production models. Results showed that groundnutseedpricevariedbetween1and2US$kg−1 forcertified andqualitydeclaredseedandbetween2and3.5US$kg−1 forearly generationseed.Overall,upto50%increaseintotalseedproduction costsresultedinreduceddropinthegrossmarginearned.However, when production costs increased by 75–100%, the gross margin droppedbyabout18%and50%inTanzaniaandinUganda,respectively. These findings indicated that groundnut seed could be providedtofarmersinremotecommunitiesatanaffordablepricewhile still keeping seed producers profitably in business. Availing these seeds to smallholder producers is a major step in achieving food securityandnutritionalhealthindevelopingcountries inSSA

Analyzing Pathways of Nurturing Informal Seed Production into Formal Private Ventures for Sustainable Seed Delivery and Crop Productivity: Experiences from Ethiopia

Sustaining crop production and productivity in sub-Saharan Africa requires the availability and use of quality seed of improved varieties by smallholder farmers. The private sector has been considered as the best way to sustain seed supply and crop productivity. Unfortunately, the private sector’s share in the seed production and delivery in sub-Saharan Africa countries has not been very substantial for decades. As a consequence, farmer access to quality seed of recently released varieties remains very low. This manuscript analyzes the experiences of informal seed producers who graduated to formal private seed enterprises to understand the effectiveness of the support they receive to become viable seed ventures. We used comparative research methods to analyze the qualitative and quantitative data collected to understand the underlying mechanisms. The findings showed that the analyzed seed enterprises started with as little as about USD 300 and have already multiplied over tenfold their initial capital. They benefited from a wide variety of supports, e.g., quality seed production, marketing, partnerships, and value chain development trainings and infrastructures, from extension workers, research centers, national and international NGOs, and the other private seed enterprise operators like large public seed enterprises and agro-dealers. The seed enterprises are producing pre-basic, basic, and certified seed of cereals and self-pollinated legume crops delivered directly to farmers, institutional markets, and agro-dealers. The seed production data have been increasing for the past three years with an area expanding from about 30 ha to over 150 ha per year for chickpea. The seed production and delivery practices being employed are smallholder farmer-based practices that are environmentally friendly. For sustainable and reliable seed production and delivery systems in sub-Saharan Africa, a bold step is needed whereby the informal seed production entities are nurtured and upgraded into formal certified seed production ventures that deliver social and economic benefits to the promotors and the communities

Genetic diversity and population structure of pigeonpea (Cajanus cajan [L.] Millspaugh) landraces grown in Benin revealed by Genotyping-By-Sequencing

Genetic diversity studies provide important details on target trait availability and its variability, for the success of breeding programs. In this study, GBS approach was used to reveal a new structuration of genetic diversity and population structure of pigeonpea in Benin. We used a total of 688 high-quality Single Nucleotide Polymorphism markers for a total of 44 pigeonpea genotypes. The distribution of SNP markers on the 11 chromosomes ranged from 14 on chromosome 5 to 133 on chromosome 2. The Polymorphism Information Content and gene diversity values were 0.30 and 0.34 respectively. The analysis of population structure revealed four clear subpopulations. The Weighted Neighbor Joining tree agreed with structure analyses by grouping the 44 genotypes into four clusters. The PCoA revealed that genotypes from subpopulations 1, 2 and 3 intermixed among themselves. The Analysis of Molecular Variance showed 7% of the total variation among genotypes while the rest of variation (93%) was within genotypes from subpopulations indicating a high gene exchange (Nm = 7.13) and low genetic differentiation (PhiPT = 0.07) between subpopulations. Subpopulation 2 presented the highest mean values of number of different alleles (Na = 1.57), number of loci with private alleles (Pa = 0.11) and the percentage of polymorphic loci (P = 57.12%). We discuss our findings and demonstrate how the genetic diversity and the population structure of this specie can be used through the Genome Wide Association Studies and Marker-Assisted Selection to enhance genetic gain in pigeonpea breeding programs in Benin

Factors Influencing Preferences and Adoption of Improved Groundnut Varieties among Farmers in Tanzania

Access and use of seed of improved varieties of groundnut among farmers can improve farmers’ livelihoods and contribute to the potential of crop production in Tanzania. This paper analyzes factors underpinning the adoption of improved groundnut varieties among farmers to pave the way for upscaling quality seed used for increased production and commodity business in farming communities. A four-stage stratified sampling was used to collect data from 300 groundnut farmers in seven agro-ecological zones through individual interviews. Secondary data were collected from the literature and the Tanzania Agricultural Research Institute at Naliendele centre (TARI–Naliendele). Descriptive statistics and Probit regression model were used for data analysis. The empirical results showed that Johari 1985, Pendo 1998, Naliendele 2009, Mnanje 2009, Mangaka 2009 and Nachi 2015, are the main six improved groundnut varieties used by farmers, with Pendo 1998 having the highest adoption rate (17.1%). In the grain market, four varieties, namely Pendo 1998, Mnanje 2009, Nachi 2015 and Johari 1985, were observed to be highly preferred by grain off-takers. Furthermore, among the adopted improved varieties, Nachi 2015, is observed to be the most consistent high yielding variety, ranging from 1100 kg/ha to 1500 kg/ha in all agro-ecological zones. A farmer’s decision to adopt new varieties is affected by age and gender, farmer group membership, availability of improved seed and seed cost. Overall, male farmers are more likely to adopt improved varieties of groundnut than female farmers. The implications of these findings are also discussed, in particular in the area of policy support

Human MUC4 mucin induces ultra-structural changes and tumorigenicity in pancreatic cancer cells.

MUC4 is a type-1 transmembrane glycoprotein and is overexpressed in many carcinomas. It is a heterodimeric protein of 930 kDa, composed of a mucin-type subunit, MUC4alpha, and a membrane-bound growth factor-like subunit, MUC4beta. MUC4 mRNA contains unique 5\u27 and 3\u27 coding sequences along with a large variable number of tandem repeat (VNTR) domain of 7-19 kb. A direct association of MUC4 overexpression has been established with the degree of invasiveness and poor prognosis of pancreatic cancer. To understand the precise role of MUC4 in pancreatic cancer, we engineered a MUC4 complementary DNA construct, mini-MUC4, whose deduced protein (320 kDa) is comparable with that of wild-type MUC4 (930 kDa) but represents only 10% of VNTR. Stable ectopic expression of mini-MUC4 in two human pancreatic cancer cell lines, Panc1 and MiaPaCa, showed that MUC4 minigene expression follows a biosynthesis and localisation pattern similar to the wild-type MUC4. Expression of MUC4 resulted in increased growth, motility, and invasiveness of the pancreatic cancer cells in vitro. Ultra-structural examination of MUC4-transfected cells showed the presence of increased number and size of mitochondria. The MUC4-expressing cells also demonstrated an enhanced tumorigenicity in an orthotopic xenograft nude mice model, further supporting a direct role of MUC4 in inducing the cancer properties. In conclusion, our results suggest that MUC4 promotes tumorigenicity and is directly involved in growth and survival of the cancer cells

Genome-wide analysis of transposon and retroviral insertions reveals preferential integrations in regions of DNA flexibility

DNA transposons and retroviruses are important transgenic tools for genome engineering. An important consideration affecting the choice of transgenic vector is their insertion site preferences. Previous large-scale analyses of Ds transposon integration sites in plants were done on the basis of reporter gene expression or germline transmission, making it difficult to discern vertebrate integration preferences. Here, we compare over 1300 Ds transposon integration sites in zebrafish, with Tol2 transposon and retroviral integration sites. Genome-wide analysis shows that Ds integration sites in the presence or absence of marker selection are remarkably similar and distributed throughout the genome. No strict motif was found, but a preference for structural features in the target DNA associated with DNA flexibility (Twist, Tilt, Rise, Roll, Shift and Slide) was observed. Remarkably, this feature is also found in transposon and retroviral integrations in maize and mouse cells. Our findings show that structural features influence integration of heterologous DNA in genomes, and have implications for targeted genome engineering