Monsanto (India)

BACKGROUND: High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource. RESULTS: Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. CONCLUSION: The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.

Consensus genetic linkage maps provide a genomic framework for quantitative trait loci identification, map-based cloning, assessment of genetic diversity, association mapping, and applied breeding in marker-assisted selection schemes. Among "orphan crops" with limited genomic resources such as cowpea [Vigna unguiculata (L.) Walp.] (2n = 2x = 22), the use of transcript-derived SNPs in genetic maps provides opportunities for automated genotyping and estimation of genome structure based on synteny analysis. Here, we report the development and validation of a high-throughput EST-derived SNP assay for cowpea, its application in consensus map building, and determination of synteny to reference genomes. SNP mining from 183,118 ESTs sequenced from 17 cDNA libraries yielded approximately 10,000 high-confidence SNPs from which an Illumina 1,536-SNP GoldenGate genotyping array was developed and applied to 741 recombinant inbred lines from six mapping populations. Approximately 90% of the SNPs were technically successful, providing 1,375 dependable markers. Of these, 928 were incorporated into a consensus genetic map spanning 680 cM with 11 linkage groups and an average marker distance of 0.73 cM. Comparison of this cowpea genetic map to reference legumes, soybean (Glycine max) and Medicago truncatula, revealed extensive macrosynteny encompassing 85 and 82%, respectively, of the cowpea map. Regions of soybean genome duplication were evident relative to the simpler diploid cowpea. Comparison with Arabidopsis revealed extensive genomic rearrangement with some conserved microsynteny. These results support evolutionary closeness between cowpea and soybean and identify regions for synteny-based functional genomics studies in legumes.

Previous studies have shown that there is considerable population structure in cultivated barley ( Hordeum vulgare L.), with the strongest structure corresponding to differences in row number and growth habit. U.S. barley breeding programs include six‐row and two‐row types and winter and spring types in all combinations. To facilitate mapping of complex traits in breeding germplasm, 1816 barley lines from 10 U.S. breeding programs were scored with 1536 single nucleotide polymorphism (SNP) genotyping assays. The number of SNPs segregating within breeding programs varied from 854 to 1398. Model‐based analysis of population structure showed the expected clustering by row type and growth habit; however, there was additional structure, some of which corresponded to the breeding programs. The model that fit the data best had seven populations: three two‐row spring, two six‐row spring, and two six‐row winter. Average linkage disequilibrium (LD) within populations decayed over a distance of 20 to 30 cM, but some populations showed long‐range LD suggestive of admixture. Genetic distance (allele‐sharing) between populations varied from 0.11 (six‐row spring vs. six‐row spring) to 0.45 (two‐row spring vs. six‐row spring). Analyses of pairwise LD revealed that the phase of allelic associations was not well correlated between populations, particularly when their allele‐sharing distance was >0.2. These results suggest that pooling divergent barley populations for purposes of association mapping may be inadvisable.

Peanut, found to be relatively drought tolerant crop, has been the choice of study to characterize the genes expressed under gradual water deficit stress. Nearly 700 genes were identified to be enriched in subtractive cDNA library from gradual process of drought stress adaptation. Further, expression of the drought inducible genes related to various signaling components and gene sets involved in protecting cellular function has been described based on dot blot experiments. Fifty genes (25 regulators and 25 functional related genes) selected based on dot blot experiments were tested for their stress responsiveness using northern blot analysis and confirmed their nature of differential regulation under different field capacity of drought stress treatments. ESTs generated from this subtracted cDNA library offered a rich source of stress-related genes including signaling components. Additional 50% uncharacterized sequences are noteworthy. Insights gained from this study would provide the foundation for further studies to understand the question of how peanut plants are able to adapt to naturally occurring harsh drought conditions. At present functional validation cannot be deemed in peanut, hence as a proof of concept seven orthologues of drought induced genes of peanut have been silenced in heterologous N. benthamiana system, using virus induced gene silencing method. These results point out the functional importance for HSP70 gene and key regulators such as Jumonji in drought stress response.

A Tnt1-insertion mutant population of Medicago truncatula ecotype R108 was screened for defects in nodulation and symbiotic nitrogen fixation. Primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. Of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. Mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (Nod-), 51 mutants with totally ineffective nodules (Nod+ Fix-), 17 mutants with partially ineffective nodules (Nod+ Fix+/-), 27 mutants defective in nodule emergence, elongation, and nitrogen fixation (Nod+/- Fix-), one mutant with delayed and reduced nodulation but effective in nitrogen fixation (dNod+/- Fix+), and 11 supernodulating mutants (Nod++Fix+/-). A total of 2,801 flanking sequence tags were generated from the 156 symbiotic mutant lines. Analysis of flanking sequence tags revealed 14 insertion alleles of the following known symbiotic genes: NODULE INCEPTION (NIN), DOESN'T MAKE INFECTIONS3 (DMI3/CCaMK), ERF REQUIRED FOR NODULATION, and SUPERNUMERARY NODULES (SUNN). In parallel, a polymerase chain reaction-based strategy was used to identify Tnt1 insertions in known symbiotic genes, which revealed 25 additional insertion alleles in the following genes: DMI1, DMI2, DMI3, NIN, NODULATION SIGNALING PATHWAY1 (NSP1), NSP2, SUNN, and SICKLE. Thirty-nine Nod- lines were also screened for arbuscular mycorrhizal symbiosis phenotypes, and 30 mutants exhibited defects in arbuscular mycorrhizal symbiosis. Morphological and developmental features of several new symbiotic mutants are reported. The collection of mutants described here is a source of novel alleles of known symbiotic genes and a resource for cloning novel symbiotic genes via Tnt1 tagging.

Leaf rust of barley is caused by the macrocyclic, heteroecious rust pathogen Puccinia hordei, with aecia reported from selected species of the genera Ornithogalum, Leopoldia, and Dipcadi, and uredinia and telia occurring on Hordeum vulgare, H. vulgare ssp. spontaneum, Hordeum bulbosum, and Hordeum murinum, on which distinct parasitic specialization occurs. Although Puccinia hordei is sporadic in its occurrence, it is probably the most common and widely distributed rust disease of barley. Leaf rust has increased in importance in recent decades in temperate barley-growing regions, presumably because of more intensive agricultural practices. Although total crop loss does not occur, under epidemic conditions yield reductions of up to 62% have been reported in susceptible varieties. Leaf rust is primarily controlled by the use of resistant cultivars, and, to date, 21 seedling resistance genes and two adult plant resistance (APR) genes have been identified. Virulence has been detected for most seedling resistance genes but is unknown for the APR genes Rph20 and Rph23. Other potentially new sources of APR have been reported, and additivity has been described for some of these resistances. Approaches to achieving durable resistance to leaf rust in barley are discussed.

Crop yield is a highly complex quantitative trait. Historically, successful breeding for improved grain yield has led to crop plants with improved source capacity, altered plant architecture, and increased resistance to abiotic and biotic stresses. To date, transgenic approaches towards improving crop grain yield have primarily focused on protecting plants from herbicide, insects, or disease. In contrast, we have focused on identifying genes that, when expressed in soybean, improve the intrinsic ability of the plant to yield more. Through the large scale screening of candidate genes in transgenic soybean, we identified an Arabidopsis thaliana B-box domain gene (AtBBX32) that significantly increases soybean grain yield year after year in multiple transgenic events in multi-location field trials. In order to understand the underlying physiological changes that are associated with increased yield in transgenic soybean, we examined phenotypic differences in two AtBBX32-expressing lines and found increases in plant height and node, flower, pod, and seed number. We propose that these phenotypic changes are likely the result of changes in the timing of reproductive development in transgenic soybean that lead to the increased duration of the pod and seed development period. Consistent with the role of BBX32 in A. thaliana in regulating light signaling, we show that the constitutive expression of AtBBX32 in soybean alters the abundance of a subset of gene transcripts in the early morning hours. In particular, AtBBX32 alters transcript levels of the soybean clock genes GmTOC1 and LHY-CCA1-like2 (GmLCL2). We propose that through the expression of AtBBX32 and modulation of the abundance of circadian clock genes during the transition from dark to light, the timing of critical phases of reproductive development are altered. These findings demonstrate a specific role for AtBBX32 in modulating soybean development, and demonstrate the validity of expressing single genes in crops to deliver increased agricultural productivity.

Consumption of broccoli has long been considered to play a role in a healthy diet. Broccoli accumulates significant amounts of the phytonutrient glucoraphanin (4-methylsulfinylbutyl glucosinolate), which is metabolized in vivo to the biologically active sulforaphane. The preponderance of evidence available from in vitro, animal, and human studies supports the association of sulforaphane with phase II enzyme induction. This has provided impetus for developing varieties of broccoli, both sprouts and whole heads, that are rich in glucoraphanin. The cancer-preventive properties of cruciferous vegetables, especially broccoli, have been studied for decades. However, evidence of broccoli directly affecting cancer incidence or progression is ambiguous, in part because of the presence of substantial polymorphisms in enzymes that metabolize sulforaphane. Since broccoli sulforaphane is one of the most potent inducers of phase II enzymes, exploration into broccoli's impact on other areas of human health, such as cardiovascular health and upper airway immunity, has been suggested. This review provides an update on evidence supporting phase II enzyme induction by sulforaphanes, with implications for breeding broccoli varieties with enhanced amounts of glucoraphanin. Early-stage human studies of consumption of broccoli with enhanced glucoraphanin are also discussed.

BACKGROUND: Bollgard(®) cotton, expressing Cry1Ac insecticidal protein, was approved for commercial planting in India in 2002, and by 2009 constituted 87% of the Indian crop, reducing losses from lepidopteran pests, including pink bollworm (PBW), Pectinophora gossypiella. Inadequate control of PBW in fields of single-gene Bollgard cotton was reported in 2009; surveys revealed heavy infestations of PBW in Bollgard, restricted to Gujarat state, but not elsewhere in India. RESULTS: Bioassays of PBW strains from Bollgard bolls showed that, while susceptible PBW could not complete development to third and later instar at 10.0 µg Cry1Ac mL(-1) , 66.1% of larvae from Gujarat Bollgard strains could. A field-resistant strain, further selected in the laboratory, had susceptibility to Cry1Ac reduced by >2000-fold. Resistance to Cry1Ac did not confer cross-resistance to the Cry2Ab2 protein. In 2010, Bollgard fields in Gujarat continued to be infested with PBW, and many Bollgard fields in the adjoining states of Maharashtra and Madhya Pradesh showed high-level infestation by PBW. CONCLUSION: Inadequate planting of refuges for PBW is the likely explanation for the field resistance to Bt cotton observed in Gujarat. These findings underscore the higher vulnerability of single-gene Bt products relative to dual-gene products expressing Cry1Ac and Cry2Ab2, and the increased risk of resistance evolution with low refuge compliance.

Abstract Rice blast, caused by fungus M agnaporthe grisea, is a serious disease causing considerable economic damage worldwide. Best way to overcome disease is to breed for disease‐resistant cultivars/parental lines of hybrids. Pusa RH 10, first aromatic, fine‐grain rice hybrid released and cultivated extensively in India. Hybrid and its parental lines, P usa 6 A and PRR 78, are highly susceptible to blast. CO 39 pyramid carrying two dominant, broad‐spectrum blast‐resistance genes, viz. Pi‐1 and Piz‐5 , used as a donor parent to introgress these genes into PRR 78 using marker‐assisted backcrossing ( MABC ). Microsatellite markers RM 5926 and AP 5659‐5 tightly linked to Pi‐1 and Piz‐5 genes, respectively, were used for foreground selection to derive introgression lines. Further, these lines were evaluated for agronomic performance, disease reaction and cooking quality traits along with PRR 78. Most of the improved lines were on par with PRR 78 for all traits evaluated except gelatinization temperature. Recurrent parent genome percentage ( RPG ) study also revealed similarity of these lines with PRR 78. Hybrids derived using improved PRR 78 lines were superior over P usa RH 10 in terms of yield.

For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.

High survivorship of pink bollworrm, Pectinophora gossypiella in bolls of Bollgard® cotton hybrids and resistance to Cry1Ac protein, expressed in Bollgard cotton were reported in field-populations collected from the state of Gujarat (western India) in 2010. We have found Cry1Ac-resistance in pink bollworm populations sourced from Bollgard and non-Bt cotton fields in the adjoining states of Maharashtra and Madhya Pradesh in Central India. Further, we observed reduced binding of labeled Cry1Ac protein to receptors localized on the brush-border membrane of pink bollworm larval strains with high tolerance to Cry1Ac. These strains were sourced from Bollgard and conventional cotton fields. A pooled Cry1Ac-resistant strain, further selected on Cry1Ac diet also showed significantly reduced binding to Cry1Ac protein. The reduced binding of Cry1Ac to receptors could be an underlying mechanism for the observed resistance in pink bollworm populations feeding on Bollgard hybrids.

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.

ATHB17 (AT2G01430) is an Arabidopsis gene encoding a member of the α-subclass of the homeodomain leucine zipper class II (HD-Zip II) family of transcription factors. The ATHB17 monomer contains four domains common to all class II HD-Zip proteins: a putative repression domain adjacent to a homeodomain, leucine zipper, and carboxy terminal domain. However, it also possesses a unique N-terminus not present in other members of the family. In this study we demonstrate that the unique 73 amino acid N-terminus is involved in regulation of cellular localization of ATHB17. The ATHB17 protein is shown to function as a transcriptional repressor and an EAR-like motif is identified within the putative repression domain of ATHB17. Transformation of maize with an ATHB17 expression construct leads to the expression of ATHB17Δ113, a truncated protein lacking the first 113 amino acids which encodes a significant portion of the repression domain. Because ATHB17Δ113 lacks the repression domain, the protein cannot directly affect the transcription of its target genes. ATHB17Δ113 can homodimerize, form heterodimers with maize endogenous HD-Zip II proteins, and bind to target DNA sequences; thus, ATHB17Δ113 may interfere with HD-Zip II mediated transcriptional activity via a dominant negative mechanism. We provide evidence that maize HD-Zip II proteins function as transcriptional repressors and that ATHB17Δ113 relieves this HD-Zip II mediated transcriptional repression activity. Expression of ATHB17Δ113 in maize leads to increased ear size at silking and, therefore, may enhance sink potential. We hypothesize that this phenotype could be a result of modulation of endogenous HD-Zip II pathways in maize.

BACKGROUND: The inheritance and phenotypic expression of resistance to Bacillus thuringiensis Cry1Ac insecticidal protein were studied in selected populations of pink bollworm, Pectinophora gossypiella (Saunders), that were collected from Bollgard cotton in India. The individual populations in the pool were Cry1Ac resistant and sourced from Cry1Ac-containing Bt cotton (Bollgard) hybrids in 2010. RESULTS: Laboratory selection on diet with 1.0 µg Cry1Ac protein mL(-1) increased the percentage reaching at least third instar from 7% in the F3 generation to 94% in the F15 generation, a 257-fold increase in median lethal concentration relative to the susceptible strain. Analysis of reciprocal genetic crosses between the Cry1Ac-resistant strain NKJ and a susceptible laboratory strain MRC showed a dominance of 0.22, indicating that the inheritance of Cry1Ac resistance is partially recessive at Cry1Ac concentrations comparable with those in Bollgard. Analyses of backcrosses of F1 hybrid moths with NKJ and MRC indicated that resistance is autosomal. The Cry1Ac-resistant strain exhibited little or no cross-resistance to the Cry2Ab2 protein. CONCLUSION: This is the first study of the dominance of Cry1Ac field resistance in P. gossypiella. The results provide the basis for refining resistance management strategies for Bt cotton.

• Grain yield reduced by 48.5–92.4% by drought from wet season to dry season.• Flowering, grain yield and harvest index were effected drastically by drought.• Dry and wet season screening is ideal to derive high yielding genotypes for drought.• Drought tolerant genotypes had low drought susceptible index and high potential yield.• 12 genotypes adapted to drought-prone rainfed lowlands in all seasons were identified.

Improving salinity and drought tolerance of crop plants has been an important aim of modern agricultural development, which depends on understanding the functions of genes expressed during the process of stress adaptation. EST resources are an efficient and cost-effective solution to gene discovery. Jatropha curcas is emerging as the most promising tree oil seed as a source of biodiesel. To identify genes that respond to abiotic stress, in the present study, we report 1240 ESTs generated from root cDNA libraries of J. curcas. ESTs were clustered and assembled into a collection of 865 unigenes, with 107 contigs and 758 singleton sequences. The putative functions of several ESTs could be assigned by similarity to plant gene sequence comparisons. It was found that 23 full-length CDS (34%) and the majority of transcription factors had sequence similarity to genes known to be involved in abiotic and biotic stress tolerance. The expression pattern of nine selected genes revealed that these genes are differentially expressed in various tissues during adaptation to stress. The data could serve as a critical resource to enable plant improvement programmes towards enhancing the adaptability of J. curcas to growth on marginal lands.

Abstract Association mapping has revolutionized human genetics and is increasingly used in plant genetics. It is an efficient way of determining the genetic basis of complex traits. In cotton so far numerous association mapping studies are available as compared to many other important crops. In our study, mapping was performed using cotton 63K infinium beadchip with 201 germplasm lines. Through fast STRUCTURE analysis, lines were grouped into 12 subgroups and revealed genome sharing among the groups. The critical value ( R 2 ) was set to 0.243 as threshold to claim LD between two loci. About 3.13% marker pairs recorded significantly high LD ( R 2 = 1), and 8.19% of marker pairs were in the range of 0.3 to 0.99 R 2 . In MLM , 349 significant marker–trait associations were detected as against 642 in GLM because of effectiveness in eliminating false associations in MLM . A total of 68 markers explained >10% phenotypic variation for yield and fibre quality traits. Phenotypic variation explained by markers was smaller, suggesting that they might be associated with minor QTL s.

Abstract Helicoverpa armigera (Hübner), Earias vittella (Fabricius), Spodoptera litura (Fabricius), Spodoptera exigua (Hübner) (all Lepidoptera: Noctuidae), Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae), and Chilo partellus (Swinhoe) (Lepidoptera: Crambidae) are the major pests of cotton and maize. Mass‐rearing of these insects under controlled conditions is necessary to obtain the numbers needed to conduct bioassays to screen insecticides, proteins, and other compounds, as tools for insect pest management. We present a diet suitable for rearing the six lepidopteran pests (five cotton and one maize pest). We further show that this diet is on par with or superior to the published diet recipes for each of the insect species, which were studied for three generations. We also discuss the advantages of antimicrobials other than formalin for keeping microbial growth under check. A combination of antimicrobial solution and benomyl provided effective control and suppressed the growth of microbes for a longer period than a formalin‐containing diet. A common diet for six pests provide opportunities for automation of diet preparation in addition to improved throughput and consistency in the process, while eliminating diet‐batch related errors.

BACKGROUND: Genetically engineered corn (Bt corn) expressing Bacillus thuringiensis Berliner insecticidal protein Cry1Ab is a biotechnological option being considered for management of lepidopteran corn pests in India. As a resistance management practice it was essential to determine the sensitivity of multiple populations of the stalk borer Chilo partellus (Swinhoe), pink borer Sesamia inferens (Walker) and the cob borer Helicoverpa armigera (Hübner) to Cry1Ab protein through bioassays. The insect populations were collected during growing seasons of Rabi 2005 (October 2005 to February 2006) and Kharif 2006 (May to September 2006). RESULTS: Multiple populations of the three lepidopteran corn pests were found to be susceptible to Cry1Ab. Median lethal concentrations (LC(50)) ranged between 0.008 and 0.068 microg Cry1Ab mL(-1) diet for 18 populations of C. partellus (across two seasons), between 0.12 and 1.99 microg mL(-1) for seven populations of H. armigera and between 0.46 and 0.56 microg mL(-1) for two populations of S. inferens. CONCLUSION: Dose-response concentrations for lethality and growth inhibition have been determined to mark baseline sensitivity of multiple populations of key lepidopteran corn pests in India to Cry1Ab protein. These benchmark values will be referenced while monitoring resistance to Cry1Ab should Bt corn hybrids expressing Cry1Ab be approved for commercial cultivation in India.