Tertiary Gene Pool Research Articles

Prolific triploid production in intersectional crosses of 4x Vaccinium corymbodendron Dunal (section Pyxothamnus) by 2x section Cyanococcus species

Vaccinium corymbodendron (section Pyxothamnus) is a tetraploid species native to high-altitude locations in Peru, Colombia, and Venezuela, and is of considerable interest because it flowers at times when nighttime temperatures drop below freezing. It also is notable for its profuse, concentrated flowering, and monopodial plant structure both of which may be useful in breeding for mechanical harvest. Initial hybridization experiments of 4x V. corymbodendron with a range of 2x species from section Cyanococcus found all hybrids were triploids. 4x × 2x crosses in conventional Vaccinium germplasm typically result in an almost absolute block of triploid offspring. The triploids expressed very low fertility as both males and females, nonetheless, several were used successfully in crosses. A single hybrid from 4x V. corymbodendron × 2x V. vitis-idaea L. (lingonberry, section Vitis-idaea) was unexpectedly found to be tetraploid and was highly fertile. These crossing results suggest V. corymbodendron either possesses no ploidy barriers to hybridization, or possesses genomic dosage factors that differ from section Cyanococcus species. Understanding these crossing relationships may open new avenues for exploitation of this germplasm and other tertiary gene pool germplasm.

Phenolics content, fruit flesh colour and browning in cultivated eggplant, wild relatives and interspecific hybrids and implications for fruit quality breeding

Increasing the content in bioactive phenolics in the eggplant (Solanum melongena) fruit is of interest, but may result in enhanced browning. We evaluated six varieties of S. melongena, 22 accessions of wild related species and 42 interspecific hybrids between cultivated eggplant and wild relatives for phenolics content, fruit flesh colour, polyphenol oxidase (PPO) activity, and fruit flesh browning. Wild relatives generally had a higher content in phenolics and a broader range of variation than cultivated eggplant. Chlorogenic acid was the predominant (>65.0%) phenolic acid in cultivated eggplant and its primary genepool wild ancestor S. insanum, while for the other wild species on average represented <50% of the chromatogram peak area. Fruit flesh colour was lighter in S. melongena than in the wild species, while PPO activity and browning was much higher in wild species of the secondary and tertiary genepools. Interspecific hybrids between S. melongena and S. insanum were intermediate in their characteristics, while those with secondary and tertiary genepool species were more similar to the wild species. No significant correlations were found between total phenolics or chlorogenic acid contents and fruit flesh browning, but PPO activity was correlated to both the degree of browning (r=0.404) and colour difference (r=0.458). The results indicate that wild species can contribute to improving the bioactive properties of eggplant without affecting negatively fruit flesh colour and browning.

World Vegetable Center Eggplant Collection: Origin, Composition, Seed Dissemination and Utilization in Breeding.

Eggplant is the fifth most economically important solanaceous crop after potato, tomato, pepper, and tobacco. Apart from the well-known brinjal eggplant (Solanum melongena L.), two other under-utilized eggplant species, the scarlet eggplant (S. aethiopicum L.) and the gboma eggplant (S. macrocarpon L.) are also cultivated. The taxonomy and identification of eggplant wild relatives is challenging for breeders due to the large number of related species, but recent phenotypic and genetic data and classification in primary, secondary, and tertiary genepools, as well as information on the domestication process and wild progenitors, facilitates their utilization in breeding. The World Vegetable Center (WorldVeg) holds a large public germplasm collection of eggplant, which includes the three cultivated species and more than 30 eggplant wild relatives, with more than 3,200 accessions collected from 90 countries. Over the last 15 years, more than 10,000 seed samples from the Center's eggplant collection have been shared with public and private sector entities, including other genebanks. An analysis of the global occurrences and genebank holdings of cultivated eggplants and their wild relatives reveals that the WorldVeg genebank holds the world's largest public collection of the three cultivated eggplant species. The composition, seed dissemination and utilization of germplasm from the Center's collection are highlighted. In recent years more than 1,300 accessions of eggplant have been characterized for yield and fruit quality parameters. Further screening for biotic and abiotic stresses in eggplant wild relatives is a priority, as is the need to amass more comprehensive knowledge regarding wild relatives' potential for use in breeding. However, as is the case for many other crops, wild relatives are highly under-represented in the global conservation system of eggplant genetic resources.

Reaction of Phaseolus spp. genotypes to ashy stem blight caused by Macrophomina phaseolina

Ashy stem blight (ASB) caused by Macrophomina phaseolina (Tassi) Goidanich (Mp) is a devastating seed-transmitted disease in common bean in the tropics. The identification of resistant cultivars throughout the cropping season contributes to disease management. Resistance is found in the primary and tertiary gene pools. Our objectives were to determine (1) the reaction of Phaseolus spp. genotypes to two Mp isolates at vegetative and reproductive stages, (2) the area under disease progress curve (AUDPC), and (3) resistant plants per genotype at harvest. Twenty-three genotypes from different origins were planted in the greenhouse in 2016 and 2017. One less-aggressive Mp (PRJD16) and one more-aggressive (PRI16) isolate were inoculated one and three times, respectively, by the cut-stem method. ‘Beniquez’, ‘Othello’, and ‘Verano’ were highly susceptible (mean scores >8.0, and AUDPC values from 264.6 to 300.8) to both isolates. BAT 477 and NY6020-4 were intermediate (5.6 and 6.2; AUDPC: 161.6 and 187.1) to PRJD16 and susceptible (7.4 and 8.2; AUDPC: 209.4 and 235.1) to PRI16. Resistant genotypes (mean scores ≤3) were not identified in this study. However, A 195, ‘Badillo’, and ‘PC 50’ possessed lower mean scores (4.3–5.4) and AUDPC values (126.4–150.9) to both isolates. Furthermore, A 195 had the highest percentage of resistant plants (55.6%) followed by PC 50, I9365-31, and PI 321637 (27.8%) to PRJD16 at harvest. Thus, the identification of resistant parents across Phaseolus species is necessary to increase the levels of ASB resistance in common bean cultivars throughout the entire cropping season.

Pairing analysis and in situ Hybridisation reveal autopolyploid-like behaviour in Solanum commersonii\xa0\xd7\xa0S. tuberosum (potato) interspecific hybrids

Wild potato relatives are rich sources of desirable traits for introgressive hybridisation into cultivated potato. One of them, Solanum commersonii (2n = 2x = 24, 1EBN, endosperm balance number), is an important species belonging to the potato tertiary genepool. It can be used in potato breeding through bridge crosses and 2n gamete production. Triploid F1 hybrids between S. commersonii (through spontaneous 2n egg formation) and diploid 2EBN Solanum tuberosum Group Phureja were crossed with S. tuberosum Group Tuberosum, resulting in successive backcross 1, 2 and 3 progenies. The main aim of this study was to determine if there are any barriers to homoeologous pairing and recombination in the allotriploid (S. commersonii × potato) hybrids and their backcrosses, and so to predict if S. commersonii chromosomes can be transmitted to the next generation and introgressed into their recipient potato chromosomes. Microscopic observations of spread pollen mother cells suggested no preferential pairing in the triploid hybrids, while chromosome transmission and segregation in further meiotic stages were fairly balanced. Fluorescent in situ hybridisation with BAC probes (BAC FISH) was used to obtain markers to trace the meiotic behaviour of specific chromosome pairs. Moreover, genomic in situ hybridisation (GISH) demonstrated no obvious differences in fluorescence signals between the homoeologues suggesting that repetitive sequences did not diverge much between the parental species. As a consequence, we were not able to trace the course of the S. commersonii chromosomes in the successive introgressive hybridisation backcross generations. Our results strongly point at a high genomic similarity between the homoeologous chromosomes promising high suitability of S. commersonii in introgressive hybridisation breeding of potato.

Genetic dissection of plant growth habit in chickpea.

A combinatorial genomics-assisted breeding strategy encompassing association analysis, genetic mapping and expression profiling is found most promising for quantitative dissection of complex traits in crop plants. The present study employed GWAS (genome-wide association study) using 24,405 SNPs (single nucleotide polymorphisms) obtained with genotyping-by-sequencing (GBS) of 92 sequenced desi and kabuli accessions of chickpea. This identified eight significant genomic loci associated with erect (E)/semi-erect (SE) vs. spreading (S)/semi-spreading (SS)/prostrate (P) plant growth habit (PGH) trait differentiation regardless of diverse desi and kabuli genetic backgrounds of chickpea. These associated SNPs in combination explained 23.8% phenotypic variation for PGH in chickpea. Five PGH-associated genes were validated successfully in E/SE and SS/S/P PGH-bearing parental accessions and homozygous individuals of three intra- and interspecific RIL (recombinant inbred line) mapping populations as well as 12 contrasting desi and kabuli chickpea germplasm accessions by selective genotyping through Sequenom MassARRAY. The shoot apical, inflorescence and floral meristems-specific expression, including upregulation (seven-fold) of five PGH-associated genes especially in germplasm accessions and homozygous RIL mapping individuals contrasting with E/SE PGH traits was apparent. Collectively, this integrated genomic strategy delineated diverse non-synonymous SNPs from five candidate genes with strong allelic effects on PGH trait variation in chickpea. Of these, two vernalization-responsive non-synonymous SNP alleles carrying SNF2 protein-coding gene and B3 transcription factor associated with PGH traits were found to be the most promising in chickpea. The SNP allelic variants associated with E/SE/SS/S PGH trait differentiation were exclusively present in all cultivated desi and kabuli chickpea accessions while wild species/accessions belonging to primary, secondary and tertiary gene pools mostly contained prostrate PGH-associated SNP alleles. This indicates strong adaptive natural/artificial selection pressure (Tajima's D 3.15 to 4.57) on PGH-associated target genomic loci during chickpea domestication. These vital leads thus have potential to decipher complex transcriptional regulatory gene function of PGH trait differentiation and for understanding the selective sweep-based PGH trait evolution and domestication pattern in cultivated and wild chickpea accessions adapted to diverse agroclimatic conditions. Collectively, the essential inputs generated will be of profound use in marker-assisted genetic enhancement to develop cultivars with desirable plant architecture of erect growth habit types in chickpea.

Breeding Perennial Grain Crops Based on Wheat

Wild relatives offer a diversity of traits potentially useful in crop improvement. Identification of major genes for resistance to biotic and abiotic stresses, in conjunction with targeted introgression, has introduced some of these traits into cultivated varieties. The difficulty of transferring complex traits, and associated linkage drag, has limited the ability of breeding programs to fully use important genetic variation. Wheat (Triticum L.) is an example of an important crop with large secondary and tertiary genepools of species capable of producing viable offspring by cross pollination. Wheat is annual, but most of the related species in the Triticeae Dumort tribe are perennials. An unknown number of genes control the perennial habit, although previous work has shown that it is a complex trait with quantitative expression. Lack of recombination between the parental genomes and complexity of the trait suggest another avenue for breeding: the addition of a genome. Multiple genera can hybridize with wheat, and some combinations produce stable amphiploids. The development of perennial grain and forage crops balancing the agronomics of wheat with the polycarpic habit of its relatives is promising. The approach is similar to Triticale (× Triticosecale Wittmack ex A. Camus), where new crops are developed combining the desirable qualities of the parents. Through prebreeding of the wild relatives, application of insight into meiosis, and strategic use of known genes, it should be more efficient to breed perennial grain crops adapted to diverse production systems.

Development of intron targeting (IT) markers specific for chromosome arm 4VS of Haynaldia villosa by chromosome sorting and next-generation sequencing

BackgroundHaynaldia villosa (L.) Schur (syn. Dasypyrum villosum L. Candargy, 2n = 14, genome VV) is the tertiary gene pool of wheat, and thus a potential resource of genes for wheat improvement. Among other, wheat yellow mosaic (WYM) resistance gene Wss1 and a take-all resistance gene were identified on the short arm of chromosome 4 V (4VS) of H. villosa. We had obtained introgressions on 4VS chromosome arm, with the objective of utilizing the target genes. However, monitoring these introgressions has been a daunting task because of inadequate knowledge as to H.villosa genome, as reflected by the lack of specific markers.ResultsThis study aims to develop 4VS-specific markers by combination of chromosome sorting and next-generation sequencing. The short arm of chromosome 4VS of H.villosa was flow-sorted using a FACSVantage SE flow cytometer and sorter, and then sequenced by Illumina sequencing. The sequence of H. villosa 4VS was assembled by the software Hecate, and then was compared with the sequence assemblies of wheat chromosome arms 4AL, 4BS and 4DS and Ae. tauschii 4DS, with the objectives of identifying exon-exon junctions and localizing introns on chromosome 4VS of H. villosa. The intron length polymorphisms suitable for designing H. villosa primers were evaluated with criteria. Consequently, we designed a total of 359 intron targeting (IT) markers, among which 232 (64.62%) markers were specific for tracing the 4VS chromatin in the wheat background.ConclusionThe combination of chromosome sorting and next-generation sequencing to develop specific IT markers for 4VS of H. villosa has high success rate and specificity, thus being applicable for the development of chromosome-specific markers for alien chromatin in wheat breeding.

Chromosome Engineering Techniques for Targeted Introgression of Rust Resistance from Wild Wheat Relatives.

Hexaploid wheat has relatively narrow genetic diversity due to its evolution and domestication history compared to its wild relatives that often carry agronomically important traits including resistance to biotic and abiotic stresses. Many genes have been introgressed into wheat from wild relatives using various strategies and protocols. One of the important issues with these introgressions is linkage drag, i.e., in addition to beneficial genes, undesirable or deleterious genes that negatively influence end-use quality and grain yield are also introgressed. Linkage drag is responsible for limiting the use of alien genes in breeding programs. Therefore, a lot of effort has been devoted to reduce linkage drag. If a gene of interest is in the primary gene pool or on a homologous chromosome from species in the secondary gene pool, it can be introgressed into common wheat by direct crosses and homologous recombination. However, if a gene of interest is on a homoeologous chromosome of a species belonging to the secondary or tertiary gene pools, chromosome engineering is required to make the transfer and to break any linkage drag. Four general approaches are used to transfer genes from homoeologous chromosomes of wild relatives to wheat chromosomes, namely, spontaneous translocations, radiation, tissue culture, and induced homoeologous recombination. The last is the method of choice provided the target gene(s) is not located near the centromere where recombination is lacking or is suppressed, and synteny between the alien chromosome carrying the gene and the recipient wheat chromosome is conserved. In this chapter, we focus on the homoeologous recombination-based chromosome engineering approach and use rust resistance genes in wild relatives of wheat as examples. The methodology will be applicable to other alien genes and other crops.

Protease inhibitors of Cajanus conferring resistance to pod borer of pigeonpea (Cajanus cajan L. Millsp.)

Pigeonpea is susceptible to pod borer damage with resistance lacking in its primary gene pool. Many Cajanus species harbor high levels of resistance. Host plant resistance can play an important role in minimizing the extent of losses due to insects and pests as well as the use of insecticides/pesticides and thus protect the environment. A major initiative was undertaken to tap the defence genes from wild relatives of secondary and tertiary gene pool through wide hybridization and thereby introgress resistance to pod borer. A range of interspecific derivatives derived from C. lanceolatus, C. cajanifolius, C. volubilis and C. platycarpus along with their parents were screened for the pod borer resistance under unprotected field conditions at ICRISAT, Patancheru, India. Biochemical basis of resistance was also identified by studying the levels of defence proteins active against bovine pancreatic trypsin, chymotrypsin and trypsin-like enzymes of H. armigera mid-gut proteases. Protease inhibitor profiles of parents and interspecific derivatives differed in terms of activity units, number and intensities of activity bands visualized on gelatin-PAGE. As the protease inhibitors are anti-nutritional factors, parents and interspecific derivatives, which resulted in high levels of Helicoverpa gut protease inhibitor (HGPI) units were screened for Human pancreatic trypsin inhibitor (HPTI) activity levels. Samples with high ratio of HGPI/HPTI represent less or no effect on human pancreatic trypsin and high effect on insect gut proteases.

Development of backcross generations and new interspecific hybrid combinations for introgression breeding in eggplant (Solanum melongena)

Introgression breeding can contribute to broadening the genetic background of eggplant (Solanum melongena). We used six eggplant varieties and 44 interspecific hybrids between these eggplant accessions and 10 accessions of wild relatives from the primary genepool species S. insanum and secondary genepool species S. anguivi, S. dasyphyllum, S. incanum, S. lichtensteinii, and S. tomentosum to obtain first backcross generations to S. melongena. Pollen viability in cultivated and wild parents and interspecific hybrids with S. insanum was high, while for interspecific hybrids with secondary genepool species it was variable. First backcross generations to S. melongena were obtained with interspecific hybrids of all the wild species, with the best results being obtained in crosses with hybrids between S. melongena and S. insanum. However, ample differences were observed among eggplant varieties in the success of the crosses. Additionally, the six eggplant varieties were crossed with secondary genepool species S. campylacanthum, S. lidii and S. vespertilio and with tertiary genepool species S. bonariense, S. elaeagnifolium and S. sisymbriifolium with the aim of obtaining new interspecific hybrids. Successful interspecific hybridization was achieved with the three new secondary genepool species tested and, using embryo rescue, with the tertiary genepool species S. elaeagnifolium. The new backcross generations and interspecific hybrids obtained will contribute to broadening the genetic background of the eggplant and to the genetic enhancement of this crop.

Harnessing Diversity in Wheat to Enhance Grain Yield, Climate Resilience, Disease and Insect Pest Resistance and Nutrition Through Conventional and Modern Breeding Approaches.

Current trends in population growth and consumption patterns continue to increase the demand for wheat, a key cereal for global food security. Further, multiple abiotic challenges due to climate change and evolving pathogen and pests pose a major concern for increasing wheat production globally. Triticeae species comprising of primary, secondary, and tertiary gene pools represent a rich source of genetic diversity in wheat. The conventional breeding strategies of direct hybridization, backcrossing and selection have successfully introgressed a number of desirable traits associated with grain yield, adaptation to abiotic stresses, disease resistance, and bio-fortification of wheat varieties. However, it is time consuming to incorporate genes conferring tolerance/resistance to multiple stresses in a single wheat variety by conventional approaches due to limitations in screening methods and the lower probabilities of combining desirable alleles. Efforts on developing innovative breeding strategies, novel tools and utilizing genetic diversity for new genes/alleles are essential to improve productivity, reduce vulnerability to diseases and pests and enhance nutritional quality. New technologies of high-throughput phenotyping, genome sequencing and genomic selection are promising approaches to maximize progeny screening and selection to accelerate the genetic gains in breeding more productive varieties. Use of cisgenic techniques to transfer beneficial alleles and their combinations within related species also offer great promise especially to achieve durable rust resistance.

Addition of Manas barley chromosome arms to the hexaploid wheat genome.

BackgroundCultivated barley belongs to the tertiary genepool of hexaploid wheat. Genes of interest can be transferred from barley into wheat through wide hybridization. The application of wheat-barley introgression lines could provide an excellent tool for the transfer of earliness, favourable amino acid composition, biotic stress resistance, abiotic stress tolerance, or good tillering ability into wheat.ResultsA set of 10 wheat-barley ditelosomic addition lines (2HS, 2HL, 3HS, 3HL, 4HS, 4HL, 6HS, 6HL, 7HS and 7HL) was developed from the progenies of an Asakaze/Manas wheat-barley hybrid produced in Martonvásár, Hungary. The addition lines were selected from self-fertilized plants of the BC2F2-BC2F4 generations using genomic in situ hybridization (GISH) and were identified by fluorescence in situ hybridization (FISH) with repetitive DNA probes [HvT01, (GAA)7 and centromere-specific (AGGGAG)4 probes]. The cytogenetic identification was confirmed using barley arm-specific SSR and STS markers. The ditelosomic additions were propagated in the phytotron and in the field, and morphological parameters (plant height, tillering, length of the main spike, number of seeds/spike and seeds/plant, and spike characteristics) were described. In addition, the salt stress response of the ditelosomic additions was determined.ConclusionsThe six-rowed winter barley cultivar Manas is much better adapted to Central European environmental conditions than the two-rowed spring barley Betzes previously used in wheat-barley crosses. The production of wheat-barley ditelosomic addition lines has a wide range of applications both for breeding (transfer of useful genes to the recipient species) and for basic research (mapping of barley genes, genetic and evolutionary studies and heterologous expression of barley genes in the wheat background).Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0393-2) contains supplementary material, which is available to authorized users.

Interspecific Hybridization between Eggplant and Wild Relatives from Different Genepools

Wild relatives represent a source of variation for many traits of interest for eggplant (Solanum melongena) breeding, as well as for broadening the genetic base of this crop. However, interspecific hybridization with wild relatives has been barely used in eggplant breeding programs. As initiation of an introgression breeding program we performed 1424 interspecific hybridizations between six accessions of eggplant from the Occidental and Oriental groups and 19 accessions of 12 wild species from the primary (Solanum incanum and Solanum insanum), secondary (Solanum anguivi, Solanum dasyphyllum, Solanum lichtensteinii, Solanum linnaeanum, Solanum pyracanthos, Solanum tomentosum, and Solanum violaceum), and tertiary (Solanum elaeagnifolium, Solanum sisymbriifolium, and Solanum torvum) genepools. Fruit set, hybrid seed, and seed germination were obtained between Solanum melongena and all wild species of the primary and secondary genepools. The highest fruit set percentage and quantity of seeds per fruit were obtained with the two primary genepool species S. incanum and S. insanum as well as with some secondary genepool species, like S. anguivi, S. dasyphyllum, or S. lichtensteinii, although some differences among species were observed depending on the direction of the hybridization. For small-fruited wild species, the number of seeds per fruit was lower when using them as maternal parent. Regarding tertiary genepool species, fruit set was obtained only in interspecific hybridizations of eggplant with S. sisymbriifolium and S. torvum, although the fruit of the former were parthenocarpic. However, it was possible to rescue viable interspecific hybrids with S. torvum. In total we obtained 58 interspecific hybrid combinations (excluding reciprocals) between eggplant and wild relatives. Some differences were observed among S. melongena accessions in the degree of success of interspecific hybridization, so that the number of hybrid combinations obtained for each accession ranged between 7 (MEL2) and 16 (MEL1). Hybridity of putative interspecific hybrid plantlets was confirmed with a morphological trait (leaf prickliness) and 12 single nucleotide polymorphism markers. The results show that eggplant is amenable to interspecific hybridization with a large number of wild species, including tertiary genepool materials. These hybrid materials are the starting point for introgression breeding in eggplant and in some cases might also be useful as rootstocks for eggplant grafting.

Interspecific hybridization to introduce useful genetic variability for pigeonpea improvement

Pigeonpea (Cajanus cajan (L.) Millspaugh) is an important grain legume grown in tropical and subtropical regions of the world. Narrow genetic base coupled with low levels of resistance against important biotic/abiotic stresses in cultivated pigeonpea is the major constraint affecting its production and productivity globally. Wild Cajanus species are the reservoir of many important genes including resistance/tolerance to diseases, insect-pests and drought, and good agronomic traits and can be utilized to improve the crop cultivars, enrich variability, and broaden the genetic base. Utilization of wild Cajanus species has contributed for the development of cytoplasmic male sterility (CMS) systems for pigeonpea improvement. Prebreeding populations involving promising wild Cajanus accessions belonging to secondary and tertiary gene pools as donors and popular pigeonpea cultivars as recipients were developed for enriching variability for pigeonpea improvement. Considerable variability was observed in these populations for morpho-agronomic traits and for biotic stresses. Two advanced backcross populations derived from wild Cajanus species are being genotyped to identify QTLs associated with agronomic traits for further deployment in pigeonpea improvement programs. Agronomically desirable and disease resistant introgression lines have been identified and shared with breeding programs for developing new high-yielding and climateresilient pigeonpea cultivars with a broad genetic base.

Landmark research for pulses improvement

This chapter reports that pulse crops (rich in protein) and cereals (rich source of carbohydrate) are an excellent combination for balanced human diet. Crop rotation of legumes with cereals enriches the soil because legumes fix nitrogen in soil in a symbiotic association with Rhyzobium species. Pulse breeders have been confined to the primary gene pool (GP-1). Exploitation of secondary (GP-2) and tertiary (GP-3) gene pools for crop improvement is hampered because of pre and post-zygotic barriers. National and international research institutes have conducted extensive plant exploration to collect primitive cultivars, land races, and wild relatives before the spread of high yielding varieties and environmental destruction eliminates them. These invaluable materials are being deposited in medium and long-term storage of gene banks. Breeders have achieved substantial gain in the yield of pulse crops by conventional breeding by producing varieties that are resistant to abiotic and biotic stresses. Breeders have produced varieties with high protein content but without antinutritional elements. Roundup Ready 2 Yield® soybean, produced through genetic transformation, has revolutionized the soybean production particularly in the United States. An example to exploit tertiary gene pool of soybean is shown. Such approach should be conducted for other legumes to broaden their genetic base.

Genetic improvement of mungbean and urdbean and their role in enhancing pulse production in India

The initial varietal development in mungbean and urdbean focused mainly on selection from landraces or the germplasm samples collected, purified and evaluated. However, systematic efforts were made by National Agricultural Research System comprising Indian Council of Agricultural Research and State Agricultural Universities through All India Coordinated Pulses Improvement Project for varietal improvement. National Bureau of Plant Genetic Resources and AICPIP centres collected over 8,000 Vigna genetic resources and also introduced germplasm from other countries and made them available for evaluation. Several resistant donors were identified and used to transfer gene(s) for biotic stresses. As a result, a number of high yielding varieties were developed through intraspecific hybridization. Large numbers of these varieties are resistant to one or more major diseases of the specific agro-eclogical niches. Six varieties in mungbean and two in urdbean were also developed through inter-specific hybridization which had new plant type and resistance to prevalent diseases. However, limited success has been achieved for the development of varieties with resistance to insect-pests and abiotic stresses. There is a need to intensify research in these areas through introgression of desirable alleles from secondary and tertiary gene pool into the cultivated type for yield, photo period and temperature insensivity and insect pest tolerance. The onset of genomics provides massive amount of information, but the success will depend on precise phenotyping to achieve desired restructuring in existing plant type.

Exploring the tertiary gene pool of bread wheat: sequence assembly and analysis of chromosome 5M(g) of Aegilops geniculata.

Next-generation sequencing (NGS) provides a powerful tool for the discovery of important genes and alleles in crop plants and their wild relatives. Despite great advances in NGS technologies, whole-genome shotgun sequencing is cost-prohibitive for species with complex genomes. An attractive option is to reduce genome complexity to a single chromosome prior to sequencing. This work describes a strategy for studying the genomes of distant wild relatives of wheat by isolating single chromosomes from addition or substitution lines, followed by chromosome sorting using flow cytometry and sequencing of chromosomal DNA by NGS technology. We flow-sorted chromosome 5M(g) from a wheat/Aegilops geniculata disomic substitution line [DS5M(g) (5D)] and sequenced it using an Illumina HiSeq2000 system at approximately 50× coverage. Paired-end sequences were assembled and used for structural and functional annotation. A total of 4236 genes were annotated on 5M(g) , in close agreement with the predicted number of genes on wheat chromosome 5D (4286). Single-gene FISH indicated no major chromosomal rearrangements between chromosomes 5M(g) and 5D. Comparing chromosome 5M(g) with model grass genomes identified synteny blocks in Brachypodium distachyon, rice (Oryza sativa), sorghum (Sorghum bicolor) and barley (Hordeum vulgare). Chromosome 5M(g) -specific SNPs and cytogenetic probe-based resources were developed and validated. Deletion bin-mapped and ordered 5M(g) SNP markers will be useful to track 5M-specific introgressions and translocations. This study provides a detailed sequence-based analysis of the composition of a chromosome from a distant wild relative of bread wheat, and opens up opportunities to develop genomic resources for wild germplasm to facilitate crop improvement.

High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool.

SummaryIn wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra‐high‐density Axiom® genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site.

Vernalization and Photoperiod Response in Annual Wild Cicer Species and Cultivated Chickpea

ABSTRACTWild Cicer species possess high levels of resistance to many stresses and can contribute to enhance levels of resistances besides broadening the genetic base of cultivated chickpea (Cicer arietinum L.). However, longer duration of wild Cicer species and nonsynchronization of flowering with cultigen remains a major deterrence for their use in chickpea improvement. In this study, the response to vernalization (V), photoperiod (P), and combination of both (V + P) was studied in terms of rate of progress toward flowering in cultivated and wild Cicer species belonging to primary, secondary, and tertiary gene pools. Both V and P treatments, alone and in combination, significantly increased the rate of progress toward flowering in wild Cicer species compared with control. Effect of P in increasing the rate of progress toward flowering was significantly higher than V in C. reticulatum Ladiz., C. echinospermum P. H. Davis, C. judaicum Boiss., C. pinnatifidum Jaub. &amp; Spach, C. bijugum Rech. f., and C. yamashitae Kitam. and vice versa in C. chorassanicum (Bunge) Popov and C. cuneatum Hochst. ex A. Rich. Synergistic effects of V and P were observed in C. bijugum, C. yamashitae, C. chorassanicum, and C. cuneatum. However, both V and P treatments had minimal effect on the rate of progress toward flowering in early‐maturing and greater effects on medium‐ and late‐maturing chickpea varieties. These results would contribute significantly to enhance use of wild Cicer species for chickpea improvement through synchronization of flowering facilitating hybridization. Also, it would improve the regeneration efficiency of wild Cicer species by genebanks and offer convenient alternate methods for rapid generation turnover.