Construction of a strawberry breeding core collection to capture and exploit genetic variation

BACKGROUND

Genetic diversity is crucial for the success of plant breeding programs and core collections are important resources to capture this diversity. Many core collections have already been constructed by gene banks, whose main goal is to obtain a panel of a limited number of genotypes to simplify management practices and to improve shareability while retaining as much diversity as possible. However, as gene banks have a different composition and goal than plant breeding programs, constructing a core collection for a plant breeding program should consider different aspects.

RESULTS

In this study, we present a novel approach for constructing a core collection by integrating both genomic and pedigree information to maximize the representation of the breeding germplasm in a minimum subset of genotypes while accounting for future genetic variation within a strawberry breeding program. Our stepwise approach starts with selecting the most important crossing parents of advanced selections and genotypes included for specific traits, to represent also future genetic variation. We then use pedigree-genomic-based relationship coefficients combined with the 'accession to nearest entry' criterion to complement the core collection and maximize its representativeness of the current breeding program. Combined pedigree-genomic-based relationship coefficients allow for accurate relationship estimation without the need to genotype every individual in the breeding program.

CONCLUSIONS

This stepwise construction of a core collection in a strawberry breeding program can be applied in other plant breeding programs to construct core collections for various purposes.

ShinyCore: An R/Shiny program for establishing core collection based on single nucleotide polymorphism data

BACKGROUND

Managing and investigating all available genetic resources are challenging. As an alternative, breeders and researchers use core collection-a representative subset of the entire collection. A good core is characterized by high genetic diversity and low repetitiveness. Among the several available software, GenoCore uses a coverage criterion that does not require computationally expensive distance-based metrics.

RESULTS

ShinyCore is a new method to select a core collection through two phases. The first phase uses the coverage criterion to quickly attain a fixed coverage, and the second phase uses a newly devised score (referred to as the rarity score) to further enhance diversity. It can attain a fixed coverage faster than a currently available algorithm devised for the coverage criterion, so it will benefit users who have big data. ShinyCore attains the minimum coverage specified by a user faster than GenoCore, and it then seeks to add entries with the rarest allele for each marker. Therefore, measures of genetic diversity and distance can be improved.

CONCLUSION

Although GenoCore is a fast algorithm, its implementation is difficult for those unfamiliar with R, ShinyCore can be easily implemented in Shiny with RStudio and an interactive web applet is available for those who are not familiar with programming languages.

Exploring genetic diversity of wild and related tetraploid wheat species Triticum turgidum and Triticum timopheevii

INTRODUCTION

The domestication bottleneck has reduced genetic diversity inwheat, necessitating the use of wild relatives in breeding programs. Wild tetraploid wheat are widely used in the breeding programs but with morphological characters, it is difficult to distinguish these, resulting in misclassification/mislabeling or duplication of accessions in the Gene bank.

OBJECTIVES

The study aims to exploreGenotyping by sequencing (GBS) to characterize wild and domesticated tetraploid wheat accessions to generate a core set of accessions to be used in the breeding program.

METHODS

TASSEL-GBS pipeline was used for SNP discovery, fastStructure was used to determine the population structure and PowerCore was used to generate a core sets. Nucleotide diversity matrices of Nie's and F-statistics (FST) index were used to determine the center of genetic diversity.

RESULTS

We found 65 % and 47 % duplicated accessions in Triticum timopheevii and T. turgidum respectively. Genome-wide nucleotide diversity and FST scan uncovered a lower intra and higher inter-species differentiation. Distinct FST regions were identified in genomic regions belonging to domestication genes: non-brittle rachis (Btr1) and vernalization (VRN-1).Our results suggest that Israel, Jordan, Syria, and Lebanonas the hub of genetic diversity of wild emmer;Turkey, and Georgia for T. durum; and Iraq, Azerbaijan, and Armenia for theT. timopheevii. Identified core set accessions preserved more than 93 % of the available genetic diversity. Genome wide association study (GWAS) indicated the potential chromosomal segment for resistance to leaf rust in T. timopheevii.

CONCLUSION

The present study explored the potential of GBS technology in data reduction while maintaining the significant genetic diversity of the species. Wild germplasm showed more differentiation than domesticated accessions, indicating the availability of sufficient diversity for crop improvement. With reduced complexity, the core set preserves the genetic diversity of the gene bank collections and will aid in a more robust characterization of wild germplasm.

The elite variations in germplasms for soybean breeding

The genetic base of soybean cultivars (Glycine max (L.) Merr.) has been narrowed through selective domestication and specific breeding improvement, similar to other crops. This presents challenges in breeding new cultivars with improved yield and quality, reduced adaptability to climate change, and increased susceptibility to diseases. On the other hand, the vast collection of soybean germplasms offers a potential source of genetic variations to address those challenges, but it has yet to be fully leveraged. In recent decades, rapidly improved high-throughput genotyping technologies have accelerated the harness of elite variations in soybean germplasm and provided the important information for solving the problem of a narrowed genetic base in breeding. In this review, we will overview the situation of maintenance and utilization of soybean germplasms, various solutions provided for different needs in terms of the number of molecular markers, and the omics-based high-throughput strategies that have been used or can be used to identify elite alleles. We will also provide an overall genetic information generated from soybean germplasms in yield, quality traits, and pest resistance for molecular breeding.

Measurements of Antibacterial Activity of Seed Crude Extracts in Cultivated Rice and Wild Oryza Species

Seeds are continuously exposed to a wide variety of microorganisms in the soil. In addition, seeds contain large amounts of carbon and nitrogen sources that support initial growth after germination. Thus, seeds in the soil can easily promote microbial growth, and seeds are susceptible to decay. Therefore, seed defense against microorganisms is important for plant survival. Seed-microbe interactions are also important issues from the perspective of food production, in seed quality and shelf life. However, seed-microbe interactions remain largely unexplored. In this study, we established a simple and rapid assay system for the antibacterial activity of rice seed crude extracts by colorimetric quantification methods by the reduction of tetrazolium compound. Using this experimental system, the diversity of effects of rice seed extracts on microbial growth was analyzed using Escherichia coli as a bacterial model. We used collections of cultivated rice, comprising 50 accessions of Japanese landraces, 52 accessions of world rice core collections, and of 30 wild Oryza accessions. Furthermore, we attempted to find genetic factors responsible for the diversity by genome-wide association analysis. Our results demonstrate that this experimental system can easily analyze the effects of seed extracts on bacterial growth. It also suggests that there are various compounds in rice seeds that affect microbial growth. Overall, this experimental system can be used to clarify the chemical entities and genetic control of seed-microbe interactions and will open the door for understanding the diverse seed-microbe interactions through metabolites.

SSR markers in revealing extent of genetic diversity and phylogenetic relationships among chickpea core collection accessions for Western Himalayas

BACKGROUND

The exploration of genetic diversity is the key source of germplasm conservation and potential to broaden its genetic base. The globally growing demand for chickpea suggests superior/climate-resilient varieties, which in turn necessitates the germplasm characterization to unravel underlying genetic variation.

METHODOLOGY AND RESULTS

A chickpea core collection comprising of diverse 192 accessions which include cultivated Cicer arietinum, and wild C. reticulatum, C. echinospermum, and C. microphyllum species were investigated to analyze their genetic diversity and relationship, by assaying 33 unlinked simple sequence repeat (SSR) markers. The results amplified a total of 323 alleles (Na), ranging from 2 to 8 with an average of 4.25 alleles per locus. Expected heterozygosity (He) differed from 0.46 to 0.86 with an average of 0.68. Polymorphic information content (PIC) ranged from 0.73 to 0.98 with an average of 0.89. Analysis of molecular variance (AMOVA) showed that most of the variation was among individuals (87%). Cluster analysis resulted in the formation of four distinct clusters. Cluster I represented all cultivated and clusters II, III, and IV comprised a heterogeneous group of cultivated and wild chickpea accessions.

CONCLUSION

We report considerable diversity and greater resolving power of SSR markers for assessing variability and interrelationship among the chickpea accessions. The chickpea core is expected to be an efficient resource for breeders for broadening the chickpea genetic base and could be useful for selective breeding of desirable traits and in the identification of target genes for genomics-assisted breeding.

Identification of superior parents with high fiber quality using molecular markers and phenotypes based on a core collection of upland cotton (Gossypium hirsutum L.)

The combination of molecular markers and phenotypes to select superior parents has become the goal of modern breeders. In this study, 491 upland cotton (Gossypium hirsutum L.) accessions were genotyped using the CottonSNP80K array and then a core collection (CC) was constructed. Superior parents with high fiber quality were identified using molecular markers and phenotypes based on the CC. The Nei diversity index, Shannon's diversity index, and polymorphism information content among chromosomes for 491 accessions ranged from 0.307 to 0.402, 0.467 to 0.587, and 0.246 to 0.316, with mean values of 0.365, 0.542, and 0.291, respectively. A CC containing 122 accessions was established and was categorized into eight clusters based on the K2P genetic distances. From the CC, 36 superior parents (including duplicates) were selected, which contained the elite alleles of markers and ranked in the top 10% of phenotypic values for each fiber quality trait. Among the 36 materials, eight were for fiber length, four were for fiber strength, nine were for fiber micronaire, five were for fiber uniformity, and ten were for fiber elongation. In particular, the nine materials, 348 (Xinluzhong34), 319 (Xinluzhong3), 325 (Xinluzhong9), 397 (L1-14), 205 (XianIII9704), 258 (9D208), 464 (DP201), 467 (DP150), and 465 (DP208), possessed the elite alleles of markers for at least two traits and could be given priority in breeding applications for a more synchronous improvement of fiber quality. The work provides an efficient method for superior parent selection and will facilitate the application of molecular design breeding to cotton fiber quality.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01300-0.

National Plant Germplasm System and construction of a melon core collection

Melon (C. melo L.) is an economically important vegetable crop cultivated worldwide. The melon collection in the U.S. National Plant Germplasm System (NPGS) is a valuable resource to conserve natural genetic diversity and provide novel traits for melon breeding. Here we use the genotyping-by-sequencing (GBS) technology to characterize 2083 melon accessions in the NPGS collected from major melon production areas as well as regions where primitive melons exist. Population structure and genetic diversity analyses suggested that C. melo ssp. melo was firstly introduced from the centers of origin, Indian and Pakistan, to Central and West Asia, and then brought to Europe and Americas. C. melo ssp. melo from East Asia was likely derived from C. melo ssp. agrestis in India and Pakistan and displayed a distinct genetic background compared to the rest of ssp. melo accessions from other geographic regions. We developed a core collection of 383 accessions capturing more than 98% of genetic variation in the germplasm, providing a publicly accessible collection for future research and genomics-assisted breeding of melon. Thirty-five morphological characters investigated in the core collection indicated high variability of these characters across accessions in the collection. Genome-wide association studies using the core collection panel identified potentially associated genome regions related to fruit quality and other horticultural traits. This study provides insights into melon origin and domestication, and the constructed core collection and identified genome loci potentially associated with important traits provide valuable resources for future melon research and breeding.

Evaluation of genetic diversity and development of core collections of industrial brewing yeast using ISSR markers

Germplasm of industrial brewing yeast of the worldwide have a richer diversity, and various successes in improving the performance of brewing yeasts. However, they are limited in that they have relatively low odds of combining desirable traits in a correct manner. To improve germplasm resource preservation, management, and utilization efficiency. In this study, the genetic diversity of 35 industrial brewing yeasts were analyzed based upon inter simple sequence repeat (ISSR) markers, in which 151 out of 167 SSR loci (90.42%) were polymorphic between two or more strains. Three preliminary core collections were established using ISSR data, and based on three different strategies as follows: an advanced maximization (M) strategy, an allele preferred sampling (A) strategy, and a random sampling (R) strategy. Comparison of genetic parameters, including polymorphic information content, Nei's genetic diversity (H), effective allele number, observed allele number, Shannon's index (I), and principal coordinate analyses, confirmed that all the core collections accurately recapitulated the diversity of the initial germplasm. Considering the loci retention ratio and trait coverage efficiency, Core1 was considered the best core collection.

Reprint of: Morphometric approaches to promote the use of exotic germplasm for improved food security and resilience to climate change: A kura clover example

Adaptation of agriculture to climate change and its associated ecological pressures will require new crops, novel trait combinations, and previously unknown phenotypic attributes to deploy in climate resilient cropping systems. Genebanks, a primary source of exotic germplasm for novel crops and breeding materials, need comprehensive methods to detect novel and unknown phenotypes without a priori information about the species or trait under consideration. We demonstrate how persistent homology (PH) and elliptical fourier descriptors (EFD), two morphometric techniques easily applied to image-based data, can serve this purpose by cataloging leaf morphology in the USDA NPGS kura clover collection and demarcating a leaf morphospace for the species. Additionally, we identify a set of representative accessions spanning the leaf morphospace and propose they serve as a kura clover core collection. The core collection will be a framework for monitoring the effects of climate change on kura clover in situ diversity and determining the role of ex situ accessions in modern agriculture.

Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies

Genebanks provide access to diverse materials for crop improvement. To utilize and evaluate them effectively, core collections, such as the World Rice Core Collection (WRC) in the Genebank at the National Agriculture and Food Research Organization, have been developed. Because the WRC consists of 69 accessions with a high degree of genetic diversity, it has been used for >300 projects. To allow deeper investigation of existing WRC data and to further promote research using Genebank rice accessions, we performed whole-genome resequencing of these 69 accessions, examining their sequence variation by mapping against the Oryza sativa ssp. japonica Nipponbare genome. We obtained a total of 2,805,329 single nucleotide polymorphisms (SNPs) and 357,639 insertion-deletions. Based on the principal component analysis and population structure analysis of these data, the WRC can be classified into three major groups. We applied TASUKE, a multiple genome browser to visualize the different WRC genome sequences, and classified haplotype groups of genes affecting seed characteristics and heading date. TASUKE thus provides access to WRC genotypes as a tool for reverse genetics. We examined the suitability of the compact WRC population for genome-wide association studies (GWASs). Heading date, affected by a large number of quantitative trait loci (QTLs), was not associated with known genes, but several seed-related phenotypes were associated with known genes. Thus, for QTLs of strong effect, the compact WRC performed well in GWAS. This information enables us to understand genetic diversity in 37,000 rice accessions maintained in the Genebank and to find genes associated with different phenotypes. The sequence data have been deposited in DNA Data Bank of Japan Sequence Read Archive (DRA) (Supplementary Table S1).

Morphometric approaches to promote the use of exotic germplasm for improved food security and resilience to climate change: a kura clover example

Adaptation of agriculture to climate change and its associated ecological pressures will require new crops, novel trait combinations, and previously unknown phenotypic attributes to deploy in climate resilient cropping systems. Genebanks, a primary source of exotic germplasm for novel crops and breeding materials, need comprehensive methods to detect novel and unknown phenotypes without a priori information about the species or trait under consideration. We demonstrate how persistent homology (PH) and elliptical Fourier descriptors (EFD), two morphometric techniques easily applied to image-based data, can serve this purpose by cataloging leaf morphology in the USDA NPGS kura clover collection and demarcating a leaf morphospace for the species. Additionally, we identify a set of representative accessions spanning the leaf morphospace and propose they serve as a kura clover core collection. The core collection will be a framework for monitoring the effects of climate change on kura clover in situ diversity and determining the role of ex situ accessions in modern agriculture.

Diversity and spatial genetic structure of natural Moroccan Quercus susber L. assessed by ISSR markers for conservation

Morocco is one of the most important regions of the world in terms of Quercus suber L. number and variation. This species is in decline due to several factors, which can lead to permanent loss of this resource. It would be essential to evaluate the genetic diversity in order to conserve maximum genetic variability of this species. The genetic diversity and differentiation of 16 sites from five regions representing the entire range of Moroccan Cork Oak were assessed. Twenty-three ISSR primers used generated 985 polymorphic fragments with an average of 42.8 bands per primer and showed 100% of polymorphism. The 173 individuals revealed a moderate level of genetic diversity at species level (I = 0.27, He = 0.161). The AMOVA showed that the highest level of diversity occurred within populations (64%), this was also confirmed by the coefficient of differentiation (Gst = 0.47). The estimated gene flow (Nm = 0.56) and the Mantel test revealed a significant correlation between geographic and genetic diversity (r = 0.266; p = 0.001). This genetic structure was further shown by the topology of the UPGMA, sPCA and STRUCTURE analysis. In addition, a core collection of 34 genotypes was established representing the essential diversity detected. This research advocates populations and individuals to preserve in order to improve and conserve this resource in the future.

Analysis of spatial distribution of genetic diversity and validation of Indian foxtail millet core collection

Foxtail millet [Setaria italica (L.) P. Beauv.] is an important small millet, grown as a short duration, drought tolerant crop across the world. This crop can be grown on wide ranges of soil conditions and has an immense potential for food and fodder in rainfed and arid regions of the India. In the present study, 31 primer pairs (27 SSR and 4 EST-SSR) were used to analyse the genetic diversity in 223 core collection accessions. Analysis resulted in detection of a total of 136 alleles with an average of 4.38 alleles per locus. Among these 136 alleles, 22 were rare, 70 were common and 44 were frequent. The PIC value ranged from 0.01 to 0.86 with an average of 0.31. The average number of observed alleles ranged from 2.0 (northern hills of India accessions) to 4.06 (exotic) with an average of 2.72. The mean Shannon's Information Index ranged from 0.44 (northern hills of India) to 0.69 (exotic) with an average of 0.52. Pair-wise Fst values indicated little to moderate genetic differentiation among the group of accessions. UPGMA clustering grouped the accessions into two major groups while analysis for population substructure indicated presence of four subpopulations. However there was no statistically well supported grouping of the accessions based on eco-geographic specificities. The core collection designated here represented substantial genetic diversity at molecular level, hence may be a good source of diversity for use in foxtail improvement programs in the region.

Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm

Background

Conservation of genetic diversity is an essential prerequisite for developing new cultivars with desirable agronomic traits. Although a large number of germplasm collections have been established worldwide, many of them face major difficulties due to large size and a lack of adequate information about population structure and genetic diversity. Core collection with a minimum number of accessions and maximum genetic diversity of pepper species and its wild relatives will facilitate easy access to genetic material as well as the use of hidden genetic diversity in Capsicum.

Results

To explore genetic diversity and population structure, we investigated patterns of molecular diversity using a transcriptome-based 48 single nucleotide polymorphisms (SNPs) in a large germplasm collection comprising 3,821 accessions. Among the 11 species examined, Capsicum annuum showed the highest genetic diversity (H_E = 0.44, I = 0.69), whereas the wild species C. galapagoense showed the lowest genetic diversity (H_E = 0.06, I = 0.07). The Capsicum germplasm collection was divided into 10 clusters (cluster 1 to 10) based on population structure analysis, and five groups (group A to E) based on phylogenetic analysis. Capsicum accessions from the five distinct groups in an unrooted phylogenetic tree showed taxonomic distinctness and reflected their geographic origins. Most of the accessions from European countries are distributed in the A and B groups, whereas the accessions from Asian countries are mainly distributed in C and D groups. Five different sampling strategies with diverse genetic clustering methods were used to select the optimal method for constructing the core collection. Using a number of allelic variations based on 48 SNP markers and 32 different phenotypic/morphological traits, a core collection ‘CC240’ with a total of 240 accessions (5.2 %) was selected from within the entire Capsicum germplasm. Compared to the other core collections, CC240 displayed higher genetic diversity (I = 0.95) and genetic evenness (J’ = 0.80), and represented a wider range of phenotypic variation (MD = 9.45 %, CR = 98.40 %).

Conclusions

A total of 240 accessions were selected from 3,821 Capsicum accessions based on transcriptome-based 48 SNP markers with genome-wide distribution and 32 traits using a systematic approach. This core collection will be a primary resource for pepper breeders and researchers for further genetic association and functional analyses.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0452-8) contains supplementary material, which is available to authorized users.

Population Structure Analysis and Selection of Core Set among Common Bean Genotypes from Jammu and Kashmir, India

Understanding the genetic diversity of a crop is useful for its effective utilization in breeding programmes. For better understanding of the genetic variability in common bean, the first and foremost step is to study its genetic diversity. In the present investigation, 138 genotypes of common bean collected from various regions of Jammu and Kashmir, India, representing major common bean growing areas of this region, were evaluated using 23 SSRs. These SSRs were found highly polymorphic and possess high values for various parameters indicating their high discriminatory power. The average PIC value observed was 0.692, with 0.730 as average gene diversity value, and 0.267 as heterozygosity. Twenty-three SSRs produced a total of 251 alleles. The dendrogram generated with un-weighted neighbour joining cluster analysis grouped genotypes into three main clusters with various degrees of sub-clustering within the clusters. The model-based STRUCTURE analysis using 23 SSR markers identified a population with 3 sub-populations which corresponds to distance-based groupings with average F _ST value and expected heterozygosity of 0.1497 and 0.6696, respectively, within the sub-population, as such high level of genetic diversity was observed within the population. Further, Core Hunter II was used to identify a core set of 96 diverse genotypes. This core set of diverse 96 genotypes is a potential resource for association mapping studies and can be used by breeders as a material to make desirable genetic crosses to generate elite varieties for the fulfilling global market needs. These findings have further implications in common bean breeding as well as conservation programs.

Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era

Background

Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remains challenging, it is important to establish practical methods to manage them. A core collection, by definition, refers to a subset of the entire population that preserves the majority of genetic diversity, enhancing the efficiency of germplasm utilization.

Results

Here, we report whole-genome resequencing of the 137 rice mini core collection or Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in the Korean genebank of the Rural Development Administration (RDA). We implemented the Illumina HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8 depths using Nipponbare as a reference. Comparisons of the sequences with the reference genome yielded more than 15 million (M) single nucleotide polymorphisms (SNPs) and 1.3 M INDELs. Phylogenetic and population analyses using 2,046,529 high-quality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that these SNPs capture evolutionary signatures that have accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for four exemplary agronomic traits in the KRIC_CORE manifest the utility of KRICE_CORE; that is, identifying previously defined genes or novel genetic factors that potentially regulate important phenotypes.

Conclusion

This study provides strong evidence that the size of KRICE_CORE is small but contains high genetic and functional diversity across the genome. Thus, our resequencing results will be useful for future breeding, as well as functional and evolutionary studies, in the post-genomic era.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2734-y) contains supplementary material, which is available to authorized users.