Methodology to establish a composite collection: case study in lentil

2006 ◽  
Vol 4 (1) ◽  
pp. 2-12 ◽  
Author(s):  
Bonnie J Furman
Keyword(s):  
Genetic Diversity ◽  
Large Scale ◽  
Dna Analysis ◽  
Agronomic Traits ◽  
Agricultural Research ◽  
Crop Improvement ◽  
Hierarchical Cluster ◽  
Wild Relatives ◽  
Crop Species ◽  
Cluster Analyses

The International Center for Agricultural Research in the Dry Areas (ICARDA) is participating in a large-scale programme, Subprogram 1 of the Consultative Group on International Agricultural Research (CGIAR) Generation Challenge Program, that aims to explore the genetic diversity of the global germplasm collections held by the CGIAR research centres. This project will identify a ‘composite collection’ of germplasm for individual crops, representing the range of diversity of each crop species and its wild relatives, and characterize each composite set using anonymous molecular markers, mainly simple sequence repeats (SSRs). The overall goal of this project is to study diversity across given genera and identify genes for resistance to biotic and abiotic stresses that can be used in crop improvement programmes. ICARDA was responsible for creating the composite collection for lentil. ICARDA has the global mandate for lentil and houses the largest global collection of this crop with 10,509 accessions. From this collection, a global composite collection of 1000 lentil accessions was established with the aim to represent genetic diversity and the agro-climatological range of lentil. Accessions for the composite collection were compiled from landraces, wild relatives, and elite germplasm and cultivars. The methodology presented here combined classical hierarchical cluster analyses using agronomic traits and two-step cluster analyses using agro-climatological data linked to the geographical coordinates of the accessions' collection sites. Genotyping for 30 SSR loci will be carried out for all 1000 accessions. Plants grown for DNA analysis will be harvested and progeny will be evaluated under field conditions at ICARDA.

scholarly journals A global barley panel revealing genomic signatures of breeding in modern cultivars

2020 ◽  
Author(s):  
Camilla Beate Hill ◽  
Tefera Tolera Angessa ◽  
Xiao-Qi Zhang ◽  
Kefei Chen ◽  
Gaofeng Zhou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Genetic Erosion ◽  
Germplasm Collection ◽  
Geographic Region ◽  
Climatic Conditions ◽  
Crop Species ◽  
Diverse Range ◽  
The Impact

AbstractThe future of plant cultivar improvement lies in the evaluation of genetic resources from currently available germplasm. Recent efforts in plant breeding have been aimed at developing new and improved varieties from poorly adapted crops to suit local environments. However, the impact of these breeding efforts is poorly understood. Here, we assess the contributions of both historical and recent breeding efforts to local adaptation and crop improvement in a global barley panel by analysing the distribution of genetic variants with respect to geographic region or historical breeding category. By tracing the impact breeding had on the genetic diversity of barley released in Australia, where the history of barley production is relatively young, we identify 69 candidate regions within 922 genes that were under selection pressure. We also show that modern Australian barley varieties exhibit 12% higher genetic diversity than historical cultivars. Finally, field-trialling and phenotyping for agriculturally relevant traits across a diverse range of Australian environments suggests that genomic regions under strong breeding selection and their candidate genes are closely associated with key agronomic traits. In conclusion, our combined dataset and germplasm collection provide a rich source of genetic diversity that can be applied to understanding and improving environmental adaptation and enhanced yields.Author summaryToday’s gene pool of crop genetic diversity has been shaped during domestication and more recently by breeding. Genetic diversity is vital for crop species to be able to adapt to changing environments. There is concern that recent breeding efforts have eroded the genetic diversity of many domesticated crops including barley. The present study assembled a global panel of barley genotypes with a focus on historical and modern Australian varieties.Genome-wide data was used to detect genes that are thought to have been under selection during crop breeding in Australian barley. The results demonstrate that despite being more extensively bred, modern Australian barley varieties exhibit higher genetic diversity than historical cultivars, countering the common perception that intensive breeding leads to genetic erosion of adaptive diversity in modern cultivars. In addition, some loci (particularly those related to phenology) were subject to selection during the introduction of other barley varieties to Australia – these genes might continue to be important targets in breeding efforts in the face of changing climatic conditions.

Genetic variation in melon (Cucumis melo L.) landraces and wild relatives of Karnataka state of southern India

2021 ◽  
pp. 1-9
Author(s):  
Manchali Shivapriya ◽  
S. Mamatha ◽  
K. Umesha ◽  
H. B. Lingaiah ◽  
S. Mohankumar
Keyword(s):  
Genetic Diversity ◽  
Cucumis Melo ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Sex Expression ◽  
Wild Relatives ◽  
Southern India ◽  
Fruit Cracking ◽  
Fruit Maturity ◽  
Karnataka State

Abstract Melon (Cucumis melo L.) is an economically important vegetable crop worldwide. Karnataka state of southern India is rich in melon landraces and wild relatives, which are potential sources of genetic diversity for crop improvement. Here we report on the collection, characterization and documentation of previously unexplored landrace and wild material to broaden the availability of this genetic diversity for use in melon improvement. Accessions of botanical groups, momordica, kachri, chandalak, reticulatus, acidulus and indicus, intermediate forms of acidulus and momordica, and three melons of an unknown group were sourced directly from farmers of eight agro-ecological regions. Twenty-three representative melon landraces and wild relatives, along with four reference varieties of different botanical groups, were evaluated for agronomic traits during the year 2016. Very wide and distinctive genetic variations were observed among the melon accessions for ovary characters, sex expression, days taken to first fruit maturity, external and internal fruit traits, and fruit cracking (splitting). The remarkable variability displayed among the melon accessions as observed from the study demonstrates the importance of them as a valuable genetic reservoir for melon improvement.

scholarly journals Molecular diversity analysis in hexaploid wheat (Triticum aestivum L.) and two Aegilops species (Aegilops crassa and Aegilops cylindrica) using CBDP and SCoT markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Ghazal Ghobadi ◽  
Alireza Etminan ◽  
Ali Mehras Mehrabi ◽  
Lia Shooshtari
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Crop Improvement ◽  
Wild Relatives ◽  
Resolving Power ◽  
Start Codon ◽  
Aegilops Cylindrica ◽  
Aegilops Crassa

Abstract Background Evaluation of genetic diversity and relationships among crop wild relatives is an important task in crop improvement. The main objective of the current study was to estimate molecular variability within the set of 91 samples from Triticum aestivum, Aegilops cylindrica, and Aegilops crassa species using 30 CAAT box–derived polymorphism (CBDP) and start codon targeted (SCoT) markers. Results Fifteen SCoT and Fifteen CBDP primers produced 262 and 298 fragments which all of them were polymorphic, respectively. The number of polymorphic bands (NPB), polymorphic information content (PIC), resolving power (Rp), and marker index (MI) for SCoT primers ranged from 14 to 23, 0.31 to 0.39, 2.55 to 7.49, and 7.56 to 14.46 with an average of 17.47, 0.34, 10.44, and 5.69, respectively, whereas these values for CBDP primers were 15 to 26, 0.28 to 0.36, 3.82 to 6.94, and 4.74 to 7.96 with a mean of 19.87, 0.31, 5.35, and 6.24, respectively. Based on both marker systems, analysis of molecular variance (AMOVA) indicated that the portion of genetic diversity within species was more than among them. In both analyses, the highest values of the number of observed (Na) and effective alleles (Ne), Nei’s gene diversity (He), and Shannon’s information index (I) were estimated for Ae. cylindrica species. Conclusion The results of cluster analysis and population structure showed that SCoT and CBDP markers grouped all samples based on their genomic constitutions. In conclusion, the used markers are very effective techniques for the evaluation of the genetic diversity in wild relatives of wheat.

scholarly journals Genetic diversity assessment of sorghum (Sorghum bicolor (L.) Moench) accessions using single nucleotide polymorphism markers

2019 ◽  
Vol 17 (5) ◽  
pp. 412-420
Author(s):  
G. Afolayan ◽  
S. P. Deshpande ◽  
S. E. Aladele ◽  
A. O. Kolawole ◽  
I. Angarawai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Diversity Assessment ◽  
Crop Research ◽  
International Crop Research Institute ◽  
Private Alleles

AbstractSorghum (Sorghum bicolor (L.) Moench) is an important resource to the national economy and it is essential to assess the genetic diversity in existing sorghum germplasm for better conservation, utilization and crop improvement. The aim of this study was to evaluate the level of genetic diversity within and among sorghum germplasms collected from diverse institutes in Nigeria and Mali using Single Nucleotide Polymorphic markers. Genetic diversity among the germplasm was low with an average polymorphism information content value of 0.24. Analysis of Molecular Variation revealed 6% variation among germplasm and 94% within germplasms. Dendrogram revealed three groups of clustering which indicate variations within the germplasms. Private alleles identified in the sorghum accessions from National Center for Genetic Resources and Biotechnology, Ibadan, Nigeria and International Crop Research Institute for the Semi-Arid Tropics, Kano, Nigeria shows their prospect for sorghum improvement and discovery of new agronomic traits. The presence of private alleles and genetic variation within the germplasms indicates that the accessions are valuable resources for future breeding programs.

scholarly journals Genetic Diversity in Commercial Rapeseed (Brassica napus L.) Varieties from Turkey as Revealed by RAPD

2013 ◽  
Vol 5 (1) ◽  
pp. 114-119 ◽  
Author(s):  
Özlem ÖZBEK ◽  
Betül Uçar GIDIK
Keyword(s):  
Genetic Diversity ◽  
Brassica Napus ◽  
Dna Analysis ◽  
Diversity Index ◽  
Principal Component ◽  
Brassica Napus L ◽  
Binary Matrix ◽  
Crop Species ◽  
Commercial Crop ◽  
The Mean

In cultivated commercial crop species, genetic diversity tends to decrease because of the extensive breeding processes. Therefore, germplasm of commercial crop species, such as Brassica napus L. should be evaluated and the genotypes, which have higher genetic diversity index, should be addressed as potential parental cross materials in breeding programs. In this study, the genetic diversity was analysed by using randomly amplified polymorphic DNA analysis (RAPD) technique in nine Turkish commercial rapeseed varieties. The RAPD primers (10-mer oligonucleotides) produced 51 scorable loci, 31 loci of which were polymorphic (60.78%) and 20 loci (39.22%) were monomorphic The RAPD bands were scored as binary matrix data and were analysed using POPGENE version 1.32. At locus level, the values of genetic diversity within population (Hs) and total (HT) were 0.15 and 0.19 respectively. The genetic differentiation (GST) and the gene flow (Nm) values between the populations were 0.20 and 2.05 respectively. The mean number of alleles (na), the mean number of effective alleles (nae), and the mean value of genetic diversity (He) were 2.00, 1.26, and 0.19 respectively. According to Pearson’s correlation, multiple regression and principal component analyses, eco-geographical conditions in combination had significant effect on genetic indices of commercial B. napus L. varieties were discussed.

Defining and identifying crop landraces

2005 ◽  
Vol 3 (3) ◽  
pp. 373-384 ◽  
Author(s):  
Tania Carolina Camacho Villa ◽  
Nigel Maxted ◽  
Maria Scholten ◽  
Brian Ford-Lloyd
Keyword(s):  
Genetic Diversity ◽  
Crop Improvement ◽  
Farming Systems ◽  
Traditional Farming ◽  
Crop Species ◽  
High Genetic Diversity ◽  
Working Definition ◽  
Landrace Diversity ◽  
Cultivated Plant ◽  
Historical Origin

Awareness of the need for biodiversity conservation is now universally accepted, but most often recent conservation activities have focused on wild species. Crop species and the diversity between and within them has significant socioeconomic as well as heritage value. The bulk of genetic diversity in domesticated species is located in traditional varieties maintained by traditional farming systems. These traditional varieties, commonly referred to as landraces, are severely threatened by genetic extinction primarily due to their replacement by modern genetically uniform varieties. The conservation of landrace diversity has been hindered in part by the lack of an accepted definition to define the entity universally recognized as landraces. Without a definition it would be impossible to prepare an inventory and without an inventory changes in landrace constituency could not be recognized over time. Therefore, based on a literature review, workshop discussion and interviews with key informants, common characteristics of landraces were identified, such as: historical origin, high genetic diversity, local genetic adaptation, recognizable identity, lack of formal genetic improvement, and whether associated with traditional farming systems. However, although these characteristics are commonly present they are not always all present for any individual landrace; several crop-specific exceptions were noted relating to crop propagation method (sexual or asexual), breeding system (self-fertilized or cross-fertilized species), length of formal crop improvement, seed management (selection or random propagation) and use. This paper discusses the characteristics that generally constitute a landrace, reviews the exceptions to these characteristics and provides a working definition of a landrace. The working definition proposed is as follows: ‘a landrace is a dynamic population(s) of a cultivated plant that has historical origin, distinct identity and lacks formal crop improvement, as well as often being genetically diverse, locally adapted and associated with traditional farming systems’.

scholarly journals Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1479
Author(s):  
Manosh Kumar Biswas ◽  
Mita Bagchi ◽  
Dhiman Biswas ◽  
Jennifer Ann Harikrishna ◽  
Yuxuan Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Comparative Mapping ◽  
In Silico ◽  
Large Scale ◽  
Crop Improvement ◽  
Musa Spp ◽  
Population Structure Analysis ◽  
A Genome ◽  
Development And Validation

Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.

scholarly journals Assessment of Genetic Diversity and Marker-Trait Associations Using Selected Early Maize Inbreds Derived From Local Landraces of Eastern Himalayan Regions

2021 ◽  
Author(s):  
E. Lamalakshmi Devi ◽  
Umakanta Ngangkham ◽  
Akoijam Ratankumar Singh ◽  
Bhuvaneswari S ◽  
Konsam Sarika ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Mean Value ◽  
Cross Combination ◽  
High Genetic Diversity ◽  
Average Value ◽  
Maize Inbreds ◽  
High Level ◽  
Trait Associations

Abstract North- Eastern parts of India fall under Eastern Himalayan region and it is a diversity hotspot of many crops including maize. Evaluation of genetic diversity is required to tape the potentiality of genetic resources in any crop improvement programmes. In the present study, genetic diversity at fifty two microsatellite markers were conducted in 30 early maize inbreds developed from local landraces of NE India. Genetic diversity analysis revealed a total of 189 alleles with a mean of 3.63 alleles/ locus. The allele size ranged from 50 bp (phi 036) to 295 bp (p 101049) which revealed a high level of genetic diversity among the loci. The PIC among the 30 genotypes ranged from 0.17 (umc 1622) to 0.76 (umc 1153) with an average value of 0.49. The value of Expected Heterozygosity (HExp) ranged from 0.19 to 0.80 with an average of 0.57, whereas the Observed Heterozygosity (HObs) ranged from 0 to 0.89 with a mean of 0.14.The genetic dissimilarity between the genotype pairs ranged from 0.40 to 0.64 with a mean value of 0.57. Cluster analysis grouped the 30 inbreds into distinct three sub-clusters. Similarly, population structure and principal coordinate analysis) analysis also classified the 30 inbred lines into three-subpopulations. AMOVA revealed that 6% of total variance is due to differences among populations, while 94% of total molecular variance is accounted by within populations. Marker-trait associations showed a total of twelve SSR markers significantly associated with seven agronomic traits. From the present finding, these results show that the thirty maize inbreds have high genetic diversity which would be useful for choosing promising parents and for making cross combination based on genetic distance and clustering for genetic improvement programmes of maize.

scholarly journals Genetic Diversity and Population Structure of Maize Inbred Lines with Varying Levels of Resistance to Striga Hermonthica Using Agronomic Trait-Based and SNP Markers

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1223
Author(s):  
Adekemi Stanley ◽  
Abebe Menkir ◽  
Agre Paterne ◽  
Beatrice Ifie ◽  
Pangirayi Tongoona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Diversity ◽  
Hierarchical Cluster ◽  
Molecular Data ◽  
Inbred Lines ◽  
Striga Hermonthica ◽  
Cluster Analyses ◽  
Maize Inbred Lines ◽  
Hierarchical Cluster Analyses

Striga hermonthica is a serious biotic stress limiting maize production in sub-Saharan Africa. The limited information on the patterns of genetic diversity among maize inbred lines derived from source germplasm with mixed genetic backgrounds limits the development of inbred lines, hybrids, and synthetics with durable resistance to S. hermonthica. This study was conducted to assess the level of genetic diversity in a panel of 150 diverse maize inbred lines using agronomic and molecular data and also to infer the population structure among the inbred lines. Ten Striga-resistance-related traits were used for the phenotypic characterization, and 16,735 high-quality single-nucleotide polymorphisms (SNPs), identified by genotyping-by-sequencing (GBS), were used for molecular diversity. The phenotypic and molecular hierarchical cluster analyses grouped the inbred lines into five clusters, respectively. However, the grouping patterns between the phenotypic and molecular hierarchical cluster analyses were inconsistent due to non-overlapping information between the phenotypic and molecular data. The correlation between the phenotypic and molecular diversity matrices was very low (0.001), which is in agreement with the inconsistencies observed between the clusters formed by the phenotypic and molecular diversity analyses. The joint phenotypic and genotypic diversity matrices grouped the inbred lines into three groups based on their reaction patterns to S. hermonthica, and this was able to exploit a broad estimate of the actual diversity among the inbred lines. The joint analysis shows an invaluable insight for measuring genetic diversity in the evaluated materials. The result indicates that wide genetic variability exists among the inbred lines and that the joint diversity analysis can be utilized to reliably assign the inbred lines into heterotic groups and also to enhance the level of resistance to Striga in new maize varieties.

scholarly journals High-quality rice RNA-seq-based co-expression network for predicting gene function and regulation

2017 ◽  
Author(s):  
Hua Yu ◽  
Bingke Jiao ◽  
Chengzhi Liang
Keyword(s):  
Large Scale ◽  
Network Inference ◽  
Agronomic Traits ◽  
Enrichment Analysis ◽  
Circular Rna ◽  
Rna Seq ◽  
Sequencing Data ◽  
High Quality ◽  
Crop Species ◽  
Functional Link

AbstractInferring the genome-scale gene co-expression network is important for understanding genetic architecture underlying the complex and various biological phenotypes. The recent availability of large-scale RNA-seq sequencing-data provides great potential for co-expression network inference. In this study, for the first time, we presented a novel heterogeneous ensemble pipeline integrating three frequently used inference methods, to build a high-quality RNA-seq-based Gene Co-expression Network (GCN) in rice, an important monocot species. The quality of the network obtained by our proposed method was first evaluated and verified with the curated positive and negative gene functional link datasets, which obviously outperformed each single method. Secondly, the powerful capability of this network for associating unknown genes with biological functions and agronomic traits was showed by enrichment analysis and case studies. Particularly, we demonstrated the potential applications of our proposed method to predict the biological roles of long non-coding RNA (lncRNA) and circular RNA (circRNA) genes. Our results provided a valuable data source for selecting candidate genes to further experimental validation during rice genetics research and breeding. To enhance identification of novel genes regulating important biological processes and agronomic traits in rice and other crop species, we released the source code of constructing high-quality RNA-seq-based GCN and rice RNA-seq-based GCN, which can be freely downloaded online at https://github.com/czllab/NetMiner.

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