CARE1, a TY3-gypsy long terminal repeat retrotransposon in the food legume chickpea (Cicer arietinum L)

We report a novel Ty3-gypsy long terminal repeat retrotransposon CARE1 (_Cicer arietinum_ retro-element 1) in chickpea. This 5920-bp AT-rich (63%) element carries 723-bp 5' and 897-bp 3' LTRs respectively flanking an internal region of 4300-bp. The LTRs of CARE1 show 93.9% nucleotide identity to each other and have 4-bp (ACTA) terminal inverted repeats. A 17-bp potential tRNAmet primer binding site downstream to 5' LTR and a 13-bp polypurine tract upstream to 3' LTR have been identified. The order of domains (Gag-proteinase-reverse transcriptase-RNaseH-integrase) in the deduced amino acid sequence and phylogenetic tree constructed using reverse transcriptase sequences places CARE1 in the gypsy group of retrotransposons. Homologues of a number of _cis_-elements including CCAAT, TATA and GT-1 have been detected in the regulatory region or the 5' LTR of CARE1. Transgenic tobacco plants containing 5' LTR:GUS construct show that its 5'-LTR is inactive in a heterologous system under normal as well as tissue culture conditions. Genomic Southern blot experiments using 5’LTR of the element as a probe show that CARE1 or its related elements are present in the genomes of various chickpea accessions from various geographic regions

Research Notes : India : Induced variability for quantitative characters

Gamma rays were used to induce the genetic variability for different quantitative characters in Bragg and Type-49 varieties of soybean. Materials and methods : Samples of 200 seeds of Bragg and Type-49 soybeans were irradiated with 10 krad, 15 krad and 20 krad doses of gamma rays, a week before planting time. These irradiated seeds, along with the unirradiated controls, were planted in split-plot design with three replications

Ensemble yield simulations: crop and climate uncertainties, sensitivity to temperature and genotypic adaptation to climate change

Estimates of the response of crops to climate change rarely quantify the uncertainty inherent in the simulation of both climate and crops. We present a crop simulation ensemble for a location in India, perturbing the response of both crop and climate under both baseline (12 720 simulations) and doubled-CO2 (171 720 simulations) climates. Some simulations used parameter values representing genotypic adaptation to mean temperature change. Firstly, observed and simulated yields in the baseline climate were compared. Secondly, the response of yield to changes in mean temperature was examined and compared to that found in the literature. No consistent response to temperature change was found across studies. Thirdly, the relative contribution of uncertainty in crop and climate simulation to the total uncertainty in projected yield changes was examined. In simulations without genotypic adaptation, most of the uncertainty came from the climate model parameters. Comparison with the simulations with genotypic adaptation and with a previous study suggested that the relatively low crop parameter uncertainty derives from the observational constraints on the crop parameters used in this study. Fourthly, the simulations were used, together with an observed dataset and a simple analysis of crop cardinal temperatures and thermal time, to estimate the potential for adaptation using existing cultivars. The results suggest that the germplasm for complete adaptation of groundnut cultivation in western India to a doubled-CO2 environment may not exist. In conjunction with analyses of germplasm and local management practices, results such as this can identify the genetic resources needed to adapt to climate change

Mini Core collection of Chickpea.

A core collection is a chosen subset of large germplasm collection that generally contains about 10% of the total accessions and represents the genetic variability of entire germplasm collection. The purpose of a core collection is to improve the use of genetic resources in crop.......

Genotyping of composite collection of foxtail millet [Setaria italica (L). P. Beauv.]

Not much information is available about the usefulness of foxtail millet germplasm in breeding programmes. A composite collection of 500 accessions has been developed and molecularly profiled using 19 SSRs (Xia et al. 2007; Dida et al. 2007; ICRISAT unpublished data) in high throughput assay (ABI3700)

Phenotypic diversity in groundnut (Arachis hypogaea L.) core collection assessed by morphological and agronomical evaluations

The groundnut (Arachis hypogaea L.) core collection consists of 1704 accessions of which 910 belong to subsp. fastigiata (var. fastigiata, vulgaris, aequatoriana, peruviana) and 794 to subsp. hypogaea (var. hypogaea, hirsuta). This core collection was evaluated for 16 morphological descriptors and for 32 agronomic characteristics, 15 in the 1999 rainy season and 17 in the 1999/2000 postrainy season, to estimate phenotypic diversity and determine importance of different descriptor traits. The two groups differed significantly for all the traits except leaflet surface and oil content. The hypogaea group showed significantly greater mean pod length, pod width, seed length, seed width, yield per plant, and 100-seed weight than the fastigiata group in both seasons whereas it is opposite for plant height, leaflet length, leaflet width and shelling percentage. There were significant phenotypic correlations among the various characteristics. Four of these, days to 50% flowering (r=0.752), leaflet length (r=0.743), pod length (r=0.758), and seed length (r=0.759) in the rainy explained more than 50% variation in the postrainy season. Principal coordinate and principal component analyses showed that 12 morphological descriptors and 15 agronomic traits, respectively, were important in explaining multivariate polymorphism. Leaflet shape and surface, colour of standard petal markings, seed colour pattern, seed width, and protein content did not significantly account for variation in the first five principal coordinates or components of fastigiata and hypogaea types as well as for the entire core collection. This indicates their relatively low importance as groundnut descriptors. The average phenotypic diversity index was similar in both subspecies groups. The Shannon-Weaver diversity index varied among traits between the two groups, and the diversity within a group depended upon the season and traits recorded

Variability for drought resistance related traits in the mini core collection of peanut

Peanut (Arachis hypogaea L.) productivity is low in the semiarid tropics mainly because of drought caused by low and erratic rainfall. Identification of genotypes that have a greater ability to use limited available water is important to enhance productivity of the crop. Water-use efficiency (WUE) is correlated with specific leaf area (SLA) and soil plant analysis development (SPAD) chlorophyll meter reading (SCMR) and both have been suggested as surrogate traits for selecting for WUE in peanut. The present study was conducted to: (i) identify genotypes with high WUE using SLA or SCMR and (ii) evaluate relationship between and relative stability of SCMR and SLA in these genotypes. The 184 mini core entries, consisting of 37 fastigiata, 58 vulgaris, 85 hypogaea, two peruviana, and one each of aequitoriana and hirsuta and four control cultivars, M 13, Gangapuri, ICGS 44 and ICGS 76 were evaluated for SLA, SCMR, and 19 vegetative, reproductive, and quality traits in the 2001 rainy and 2001–2002 postrainy seasons at ICRISAT Center. Data were analyzed by REML analysis. Seasons were significant for all traits. Variances due to genotypes were significant for SCMR and SLA at 60 and 80 d after sowing (DAS) and other traits except pods per plant, yield per plant, haulm yield per plot, and protein and oil contents. The genotype x season interactions were significant for both SCMR and SLA at 80 DAS only and for all other quantitative traits except number of primary branches, and pod width. The SCMR values at different stages and seasons were more positively correlated with each other than the correlation of SLA values together. SCMR and SLA were negatively correlated. SCMR values were more strongly correlated with pod yield and other economic traits such as 100-seed weight at both 60 and 80 DAS than SLA. On the basis of higher heritability and lower proportion of genotype x season interaction variance to phenotypic variance, SCMR appeared to be more stable than SLA. On the basis of SLA and SCMR values compared with the control cultivar, five vulgaris and 13 hypogaea accessions were selected. These accessions and control cultivars were grouped by scores of the first 15 principal components (PCs). The clustering by UPGMA method indicated that the selected accessions were diverse from the control cultivars and can be used in the peanut improvement programs to develop cultivars with a broad genetic base

Wet or dry? Impact of conditioning seed in germplasm conservation strategies

Seed deterioration is a continuous process and we need techniques that prolong longevity. A combination of 3-7% seed moisture content (mc) and a storage temperature below 0°C is suitable for long-term preservation of germplasm samples. When crop seeds are dried to low moisture levels, they decrease in weight and volume, and might develop seed coat cracks if dried too rapidly. Dried seeds are susceptible to mechanical injuries, especially when they absorb water too quickly, and suffer what is called imbibition injury

Composite collection of Chickpea

Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. ICRISAT and ICARDA jointly developed a composite collection of 3000 accessions, which consists of 1956 accessions of the ICRISAT core collection, 709 accessions from ICARDA, 39 advanced lines/cultivars, 35 distinct morphological variants, 20 accessions from wild Cicer species (C. reticulatum and C. echinospermum), and 241 trait-specific (resistance to biotic and abiotic stresses, early maturity, multi-seeded pods, double podded, large-seed, high seed protein, nodulation and responsive to high input conditions) accessions. Biologically, it represents 80% land races, 11% advanced lines/cultivars, 1% wild species, and 8% accessions of unknown origin. This composite collection has been molecularly profiled using 50 SSRs in high throughput assay (ABI3700)