A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley ( Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, ...1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3'-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5'-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 +/- 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity.
Expressed sequence tag (EST) projects have generated a vast amount of publicly available sequence data from plant species; these data can be mined for simple sequence repeats (SSRs). These SSRs are ...useful as molecular markers because their development is inexpensive, they represent transcribed genes and a putative function can often be deduced by a homology search. Because they are derived from transcripts, they are useful for assaying the functional diversity in natural populations or germplasm collections. These markers are valuable because of their higher level of transferability to related species, and they can often be used as anchor markers for comparative mapping and evolutionary studies. They have been developed and mapped in several crop species and could prove useful for marker-assisted selection, especially when the markers reside in the genes responsible for a phenotypic trait. Applications and potential uses of EST-SSRs in plant genetics and breeding are discussed.
Vast germplasm collections are accessible but their use for crop improvement is limited—efficiently accessing genetic diversity is still a challenge. Molecular markers have clarified the structure of ...genetic diversity in a broad range of crops. Recent developments have made whole-genome surveys and gene-targeted surveys possible, shedding light on population dynamics and on the impact of selection during domestication. Thanks to this new precision, germplasm description has gained analytical power for resolving the genetic basis of trait variation and adaptation in crops such as major cereals, chickpea, grapevine, cacao, or banana. The challenge now is to finely characterize all the facets of plant behavior in carefully chosen materials. We suggest broadening the use of ‘core reference sets’ so as to facilitate material sharing within the scientific community.
Genomics research is generating new tools, such as functional molecular markers and informatics, as well as new knowledge about statistics and inheritance phenomena that could increase the efficiency ...and precision of crop improvement. In particular, the elucidation of the fundamental mechanisms of heterosis and epigenetics, and their manipulation, has great potential. Eventually, knowledge of the relative values of alleles at all loci segregating in a population could allow the breeder to design a genotype
in silico and to practice whole genome selection. High costs currently limit the implementation of genomics-assisted crop improvement, particularly for inbreeding and/or minor crops. Nevertheless, marker-assisted breeding and selection will gradually evolve into ‘genomics-assisted breeding’ for crop improvement.
Cultivated groundnut or peanut (
Arachis hypogaea
L.), an allotetraploid (2
n
= 4
x
= 40), is a self pollinated and widely grown crop in the semi-arid regions of the world. Improvement of drought ...tolerance is an important area of research for groundnut breeding programmes. Therefore, for the identification of candidate QTLs for drought tolerance, a comprehensive and refined genetic map containing 191 SSR loci based on a single mapping population (TAG 24 × ICGV 86031), segregating for drought and surrogate traits was developed. Genotyping data and phenotyping data collected for more than ten drought related traits in 2–3 seasons were analyzed in detail for identification of main effect QTLs (M-QTLs) and epistatic QTLs (E-QTLs) using QTL Cartographer, QTLNetwork and Genotype Matrix Mapping (GMM) programmes. A total of 105 M-QTLs with 3.48–33.36% phenotypic variation explained (PVE) were identified using QTL Cartographer, while only 65 M-QTLs with 1.3–15.01% PVE were identified using QTLNetwork. A total of 53 M-QTLs were such which were identified using both programmes. On the other hand, GMM identified 186 (8.54–44.72% PVE) and 63 (7.11–21.13% PVE), three and two loci interactions, whereas only 8 E-QTL interactions with 1.7–8.34% PVE were identified through QTLNetwork. Interestingly a number of co-localized QTLs controlling 2–9 traits were also identified. The identification of few major, many minor M-QTLs and QTL × QTL interactions during the present study confirmed the complex and quantitative nature of drought tolerance in groundnut. This study suggests deployment of modern approaches like marker-assisted recurrent selection or genomic selection instead of marker-assisted backcrossing approach for breeding for drought tolerance in groundnut.
Pure line breeding is a resource-intensive activity that takes 10 years or more to develop a new cultivar. In some crops, conducting off-season nurseries has significantly reduced the length of the ...breeding cycle. This approach could not be exploited in pigeonpea
Cajanus cajan
(L.) Millsp., because traditionally it has been a photoperiod-sensitive crop that requires long periods of darkness to induce flowering. However, the recent success of breeding early maturing photoperiod-insensitive genotypes has opened up the possibility of adopting ‘speed breeding’ techniques to enable rapid generation turnover. This paper outlines a speed breeding approach that integrates the use of immature seed germination for rapid generation advancement and a “single pod descent” method of breeding. To accelerate line development, while conserving genetic variability, the approach permits four generations per year and can fast-track field evaluation of resulting homozygous lines. Therefore, the breeding strategy conserves resources and has potential to deliver new early maturing cultivars within a substantially reduced timeframe of 4–5 years.
This open access book shares impact stories – testimonies from various value chain actors who have been part of the Tropical Legumes (TL) projects, over the past twelve years. The Tropical Legumes ...projects led by ICRISAT in three parts (TLI, TLII and TLIII), constitute a major international initiative supported by the Bill & Melinda Gates Foundation (BMGF) and jointly implemented by the International Center for Tropical Agriculture (CIAT), International Institute of Tropical Agriculture (IITA) and National Agricultural Research Systems (NARS) partners from Sub-Saharan Africa and India. The project developed improved cultivars of common bean, cowpea, chickpea and groundnut (but also soya bean and pigeon pea cultivars in its initial phases) and delivers their seed to smallholders in BMGF-focus areas. It also strengthens the NARS and CGIAR's breeding programs and seed platforms to enhance their ability to deliver high and sustained outputs to smallholder farmers. The book compiles the experiences of a diversity of actors within the grain legume value chains, with a focus on groundnut and common beans in Tanzania and Uganda, groundnut and cowpea in Nigeria, and groundnut in Ghana. All stakeholders involved share their thoughts on being part of a decade-long development project family. National agricultural research institutes, knowledge brokering organizations, NGOs, public and private seed companies, agro-dealers, individual seed entrepreneurs, farm-implement makers, farmer cooperatives, farmer groups, individual men and women farmers, middlemen, processors, traders and consumers were all involved in this project, and as such this book provides valuable insights for development workers, technical staff, and project managers.
The main objective of the present study was to isolate and characterize actinomycetes for their plant growth-promotion in chickpea. A total of 89 actinomycetes were screened for their antagonism ...against fungal pathogens of chickpea by dual culture and metabolite production assays. Four most promising actinomycetes were evaluated for their physiological and plant growth-promotion properties under in vitro and in vivo conditions. All the isolates exhibited good growth at temperatures from 20°C to 40°C, pH range of 7–11 and NaCl concentrations up to 8%. These were also found highly tolerant to Bavistin, slightly tolerant to Thiram and Captan (except VAI-7 and VAI-40) but susceptible to Benlate and Ridomil at field application levels and were found to produce siderophore, cellulase, lipase, protease, chitinase (except VAI-40), hydrocyanic acid (except VAI-7 and VAI-40), indole acetic acid and β-1,3-glucanase. When the four actinomycetes were evaluated for their plant growth-promotion properties under field conditions on chickpea, all exhibited increase in nodule number, shoot weight and yield. The actinomycetes treated plots enhanced total N, available P and organic C over the un-inoculated control. The scanning electron microscope studies exhibited extensive colonization by actinomycetes on the root surface of chickpea. The expression profiles for indole acetic acid, siderophore and β-1,3-glucanase genes exhibited up-regulation for all three traits and in all four isolates. The actinomycetes were identified as Streptomyces but different species in the 16S rDNA analysis. It was concluded that the selected actinomycetes have good plant growth-promotion and biocontrol potentials on chickpea.
•Silicon-on-nitride slot waveguide-based evanescent field absorption-gas sensing scheme exploiting mid-IR fingerprint regime is proposed.•Numerical demonstration of the detection of NH3 gas in ...atmosphere operating at 3μm is analyzed.•With optimized waveguide structure, maximum achievable evanescent field fraction becomes ∼43%.•Feasible detection up to 5ppm level with a waveguide length of just 8.7mm.•Various fabrication tolerances are examined in detail and proposed structure has the potential for chip-scale trace gas sensing.
We propose design of a chip-scale evanescent field absorption-based trace gas sensor, exploiting silicon-on-nitride (SON) slot waveguide structure at mid-IR wavelength region. As an example, we numerically demonstrate detectability of NH3 gas in the atmosphere at its characteristic absorption wavelength of 3μm. Using the optimum sensor design, detection down to 5ppm including loss is viable in just ∼8.7mm length of the proposed slot waveguide. The achievable evanescent field fraction (η) is upto ∼43%. Our tolerance studies show that η is relatively more critical to the slot width as compared to its height.
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