Optimizing speed breeding and seed/pod chip based genotyping techniques in pigeonpea: A way forward for high throughput line development
Ontology highlight
ABSTRACT:
SUBMITTER: Gangashetty P
PROVIDER: S-EPMC10865548 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Pigeonpea is the second most important pulse legume crop for food and nutritional security of South Asia that requires accelerated breeding using high throughput genomic tools. Single nucleotide polymorphisms (SNPs) are highly suitable markers for this purpose because of their bi-allelic nature, reproducibility and high abundance in the genome. Here we report on development and use of a pigeonpea 62 K SNP chip array 'CcSNPnks' for Affymetrix GeneTitan® platform. The array was designed after filtering 645,662 genic-SNPs identified by re-sequencing of 45 diverse genotypes and has 62,053 SNPs from 9629 genes belonging to five different categories, including 4314 single-copy genes unique to pigeonpea, 4328 single-copy genes conserved between soybean and pigeonpea, 156 homologs of agronomically important cloned genes, 746 disease resistance and defense response genes and 85 multi-copy genes of pigeonpea. This fully genic chip has 28.94% exonic, 33.04% intronic, 27.56% 5'UTR and 10.46% 3'UTR SNPs and incorporates multiple SNPs per gene allowing gene haplotype network analysis. It was used successfully for the analysis of genetic diversity and population structure of 95 pigeonpea varieties and high resolution mapping of 11 yield related QTLs for number of branches, pod bearing length and number of seeds per pod in a biparental RIL population. As an accurate high-density genotyping tool, 'CcSNPnks' chip array will be useful for high resolution fingerprinting, QTL mapping and genome wide as well as gene-based association studies in pigeonpea.
| S-EPMC7080765 | biostudies-literature
Project description:Root and tuber crop breeding is at the front and center of CIP's science program, which seeks to develop and disseminate sustainable agri-food technologies, information and practices to serve objectives including poverty alleviation, income generation, food security and the sustainable use of natural resources. CIP was established in 1971 in Peru, which is part of potato's center of origin and diversity, with an initial mandate on potato and expanding to include sweetpotato in 1986. Potato and sweetpotato are among the top 10 most consumed food staples globally and provide some of the most affordable sources of energy and vital nutrients. Sweetpotato plays a key role in securing food for many households in Africa and South Asia, while potato is important worldwide. Both crops grow in a range of conditions with relatively few inputs and simple agronomic techniques. Potato is adapted to the cooler environments, while sweetpotato grows well in hot climates, and hence, the two crops complement each other. Germplasm enhancement (pre-breeding), the development of new varieties and building capacity for breeding and variety testing in changing climates with emphasis on adaptation, resistance, nutritional quality and resource-use efficiency are CIP's central activities with significant benefits to the poor. Investments in potato and sweetpotato breeding and allied disciplines at CIP have resulted in the release of many varieties some of which have had documented impact in the release countries. Partnership with diverse types of organizations has been key to the centers way of working toward improving livelihoods through crop production in the global South.
| S-EPMC10730645 | biostudies-literature
Project description:In most crop breeding programs, the rate of yield increment is insufficient to cope with the increased food demand caused by a rapidly expanding global population. In plant breeding, the development of improved crop varieties is limited by the very long crop duration. Given the many phases of crossing, selection, and testing involved in the production of new plant varieties, it can take one or two decades to create a new cultivar. One possible way of alleviating food scarcity problems and increasing food security is to develop improved plant varieties rapidly. Traditional farming methods practiced since quite some time have decreased the genetic variability of crops. To improve agronomic traits associated with yield, quality, and resistance to biotic and abiotic stresses in crop plants, several conventional and molecular approaches have been used, including genetic selection, mutagenic breeding, somaclonal variations, whole-genome sequence-based approaches, physical maps, and functional genomic tools. However, recent advances in genome editing technology using programmable nucleases, clustered regularly interspaced short palindromic repeats (CRISPR), and CRISPR-associated (Cas) proteins have opened the door to a new plant breeding era. Therefore, to increase the efficiency of crop breeding, plant breeders and researchers around the world are using novel strategies such as speed breeding, genome editing tools, and high-throughput phenotyping. In this review, we summarize recent findings on several aspects of crop breeding to describe the evolution of plant breeding practices, from traditional to modern speed breeding combined with genome editing tools, which aim to produce crop generations with desired traits annually.
| S-EPMC7177917 | biostudies-literature
Project description:The contribution of fungal infections to the morbidity and mortality of HIV-infected individuals is largely unrecognized. A recent meeting highlighted several priorities that need to be urgently addressed, including improved epidemiological surveillance, increased availability of existing diagnostics and drugs, more training in the field of medical mycology, and better funding for research and provision of treatment, particularly in developing countries.
| S-EPMC4129449 | biostudies-literature
Project description:Seed development is an important event in plant life cycle that has interested humankind since ages, especially in crops of economic importance. Pigeonpea is an important grain legume of the semi-arid tropics, used mainly for its protein rich seeds. In order to understand the transcriptional programming during the pod and seed development, RNA-seq data was generated from embryo sac from the day of anthesis (0 DAA), seed and pod wall (5, 10, 20 and 30 DAA) of pigeonpea variety "Asha" (ICPL 87119) using Illumina HiSeq 2500. About 684 million sequencing reads have been generated from nine samples, which resulted in the identification of 27,441 expressed genes after sequence analysis. These genes have been studied for their differentially expression, co-expression, temporal and spatial gene expression. We have also used the RNA-seq data to identify important seed-specific transcription factors, biological processes and associated pathways during seed development process in pigeonpea. The comprehensive gene expression study from flowering to mature pod development in pigeonpea would be crucial in identifying candidate genes involved in seed traits directly or indirectly related to yield and quality. The dataset will serve as an important resource for gene discovery and deciphering the molecular mechanisms underlying various seed related traits.
| S-EPMC5070767 | biostudies-literature
Project description:Pigeonpea is an important pulse crop grown predominantly in the tropical and sub-tropical regions of the world. Although pigeonpea growing area has considerably increased, yield has remained stagnant for the last six decades mainly due to the exposure of the crop to various biotic and abiotic constraints. In addition, low level of genetic variability and limited genomic resources have been serious impediments to pigeonpea crop improvement through modern breeding approaches. In recent years, however, due to the availability of next generation sequencing and high-throughput genotyping technologies, the scenario has changed tremendously. The reduced sequencing costs resulting in the decoding of the pigeonpea genome has led to the development of various genomic resources including molecular markers, transcript sequences and comprehensive genetic maps. Mapping of some important traits including resistance to Fusarium wilt and sterility mosaic disease, fertility restoration, determinacy with other agronomically important traits have paved the way for applying genomics-assisted breeding (GAB) through marker assisted selection as well as genomic selection (GS). This would accelerate the development and improvement of both varieties and hybrids in pigeonpea. Particularly for hybrid breeding programme, mitochondrial genomes of cytoplasmic male sterile (CMS) lines, maintainers and hybrids have been sequenced to identify genes responsible for cytoplasmic male sterility. Furthermore, several diagnostic molecular markers have been developed to assess the purity of commercial hybrids. In summary, pigeonpea has become a genomic resources-rich crop and efforts have already been initiated to integrate these resources in pigeonpea breeding.
| S-EPMC4330709 | biostudies-literature
Project description:CGH was used to compare induced structural variation among soybean fast neutron lines, developed in background M92-220.
2011-08-02 | GSE31038 | GEO
Project description:For a number of years it has been widely assumed that measurement of serum 25-hydroxyvitamin D [25(OH)D] concentration is the best approach to assessing an individual's vitamin D status. However, it has also been recognized that there is substantial within-assay variation in 25(OH)D measurement and even greater between-assay variability. Such assay variation clearly confounds attempts to define what constitutes the diagnosis of hypovitaminosis D. Importantly, assay variability makes pooling of 25(OH)D results from different studies in systematic reviews for the specific purpose of determining dose-response and/or clinical cut points at best problematic. Therefore, to develop and implement evidence-based clinical guidelines, it is essential that 25(OH)D measurement be standardized in both clinical and research laboratories. In this Perspective we outline a way forward toward achieving this goal-the Vitamin D Standardization Program (VDSP).
| S-EPMC5443565 | biostudies-literature
Project description:The Genome 10K Project was established in 2009 by a consortium of biologists and genome scientists determined to facilitate the sequencing and analysis of the complete genomes of 10,000 vertebrate species. Since then the number of selected and initiated species has risen from ?26 to 277 sequenced or ongoing with funding, an approximately tenfold increase in five years. Here we summarize the advances and commitments that have occurred by mid-2014 and outline the achievements and present challenges of reaching the 10,000-species goal. We summarize the status of known vertebrate genome projects, recommend standards for pronouncing a genome as sequenced or completed, and provide our present and future vision of the landscape of Genome 10K. The endeavor is ambitious, bold, expensive, and uncertain, but together the Genome 10K Consortium of Scientists and the worldwide genomics community are moving toward their goal of delivering to the coming generation the gift of genome empowerment for many vertebrate species.
| S-EPMC5837290 | biostudies-literature
Project description:BACKGROUND:With India preparing for the next decennial Census in 2021, we compared the disability estimates and data collection methodology between the Census 2011 and the most recent population-level survey for India and its states, to highlight the issues to be addressed to improve robustness of the disability estimates in the upcoming Census. METHODS:Data from the Census 2011 and from two complementary nationally representative household surveys that covered all Indian states with the same methodology and survey instruments-the District-Level Household Survey-4 (DLHS-4, 2012-2013) and the Annual Health Surveys (AHS three rounds, 2010-11, 2011-12 and 2012-13) were used. Data from DLHS-4 and AHS 2012-13 round were pooled to generate estimates for the year 2012-13. Data collection methodology between the sources was compared, including the review of definitions of each type of disability. The overall, mental, visual, hearing, speech, and movement disability rate (DR) per 100,000 population were compared between the sources for India and for each state, and the percent difference in the respective rates was calculated. We explored the reliability of these estimates comparing yearly data from the AHS for three successive rounds. RESULTS:Survey data were collected through proxy reporting, however, it is not entirely clear whether the data were proxy- or self-reported or a mix of both in the Census. The overall DR was 25.1% higher in the Census (2,242; 95% CI 2,241-2,243) than the survey (1,791; 95% CI 1,786-1,797) per 100,000 population, with the state-level difference ranging from -64% in Tamil Nadu to 107% in Sikkim state. Despite both sources using nearly similar definitions for overall disability and disability by type, the difference in DR was 125.5%, 54.2%, -25.7%, -19.7%, and 21.9% for hearing, speech, mental, movement, and visual DR, respectively. At the state-level, the difference in disability-specific estimates ranged from -84% to 450%. The extent of variations in the disability-specific estimates in AHS successive rounds ranged from -25% to 929% at the state-level. CONCLUSIONS:There is momentum globally towards building disability measurement that is consistent with the data required for monitoring of the Sustainable Development Goals to ensure robust estimation of disability. The current estimates from the Census and surveys seem much lower than would be expected at the population level. We make recommendations that India needs to take serious note of in order to improve the validity and reliability of India's disability estimates.
| S-EPMC6730860 | biostudies-literature