The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections

Double-digest restriction-associated DNA sequencing-based genotyping and its applications in sesame germplasm management

Sesame (Sesamum indicum L.) is an ancient oilseed crop belonging to the family Pedaliaceae and a globally cultivated crop for its use as oil and food. In this study, 2496 sesame accessions, being conserved at the National Genebank of ICAR-National Bureau of Plant Genetic Resources (NBPGR), were genotyped using genomics-assisted double-digest restriction-associated DNA sequencing (ddRAD-seq) approach. A total of 64,910 filtered single-nucleotide polymorphisms (SNPs) were utilized to assess the genome-scale diversity. Applications of this genome-scale information (reduced representation using restriction enzymes) are demonstrated through the development of a molecular core collection (CC) representing maximal SNP diversity. This information is also applied in developing a mid-density panel (MDP) comprising 2515 hyper-variable SNPs, representing almost equally the genic and non-genic regions. The sesame CC comprising 384 accessions, a representative set of accessions with maximal diversity, was identified using multiple criteria such as k-mer (subsequence of length "k" in a sequence read) diversity, observed heterozygosity, CoreHunter3, GenoCore, and genetic differentiation. The coreset constituted around 15% of the total accessions studied, and this small subset had captured >60% SNP diversity of the entire population. In the coreset, the admixture analysis shows reduced genetic complexity, increased nucleotide diversity (π), and is geographically distributed without any repetitiveness in the CC germplasm. Within the CC, India-originated accessions exhibit higher diversity (as expected based on the center of diversity concept), than those accessions that were procured from various other countries. The identified CC set and the MDP will be a valuable resource for genomics-assisted accelerated sesame improvement program.

Recent advances in genome editing strategies for balancing growth and defence in sugarcane (Saccharum officinarum)

Sugarcane (Saccharum officinarum ) has gained more attention worldwide in recent decades because of its importance as a bioenergy resource and in producing table sugar. However, the production capabilities of conventional varieties are being challenged by the changing climates, which struggle to meet the escalating demands of the growing global population. Genome editing has emerged as a pivotal field that offers groundbreaking solutions in agriculture and beyond. It includes inserting, removing or replacing DNA in an organism's genome. Various approaches are employed to enhance crop yields and resilience in harsh climates. These techniques include zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats/associated protein (CRISPR/Cas). Among these, CRISPR/Cas is one of the most promising and rapidly advancing fields. With the help of these techniques, several crops like rice (Oryza sativa ), tomato (Solanum lycopersicum ), maize (Zea mays ), barley (Hordeum vulgare ) and sugarcane have been improved to be resistant to viral diseases. This review describes recent advances in genome editing with a particular focus on sugarcane and focuses on the advantages and limitations of these approaches while also considering the regulatory and ethical implications across different countries. It also offers insights into future prospects and the application of these approaches in agriculture.

Genetic diversity, population structure, and selection of breeder germplasm subsets from the USDA sweetpotato (Ipomoea batatas) collection

Sweetpotato (Ipomoea batatas) is the sixth most important food crop and plays a critical role in maintaining food security worldwide. Support for sweetpotato improvement research in breeding and genetics programs, and maintenance of sweetpotato germplasm collections is essential for preserving food security for future generations. Germplasm collections seek to preserve phenotypic and genotypic diversity through accession characterization. However, due to its genetic complexity, high heterogeneity, polyploid genome, phenotypic plasticity, and high flower production variability, sweetpotato genetic characterization is challenging. Here, we characterize the genetic diversity and population structure of 604 accessions from the sweetpotato germplasm collection maintained by the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Plant Genetic Resources Conservation Unit (PGRCU) in Griffin, Georgia, United States. Using the genotyping-by-sequencing platform (GBSpoly) and bioinformatic pipelines (ngsComposer and GBSapp), a total of 102,870 polymorphic SNPs with hexaploid dosage calls were identified from the 604 accessions. Discriminant analysis of principal components (DAPC) and Bayesian clustering identified six unique genetic groupings across seven broad geographic regions. Genetic diversity analyses using the hexaploid data set revealed ample genetic diversity among the analyzed collection in concordance with previous analyses. Following population structure and diversity analyses, breeder germplasm subsets of 24, 48, 96, and 384 accessions were established using K-means clustering with manual selection to maintain phenotypic and genotypic diversity. The genetic characterization of the PGRCU sweetpotato germplasm collection and breeder germplasm subsets developed in this study provide the foundation for future association studies and serve as precursors toward phenotyping studies aimed at linking genotype with phenotype.

Core Collections: Is There Any Value for Cotton Breeding?

Global plant breeding activities are reliant on the available genetic variation held in extant varieties and germplasm collections. Throughout the mid- to late 1900s, germplasm collecting efforts were prioritized for breeding programs to archive precious material before it disappeared and led to the development of the numerous large germplasm resources now available in different countries. In recent decades, however, the maintenance and particularly the expansion of these germplasm resources have come under threat, and there has been a significant decline in investment in further collecting expeditions, an increase in global biosecurity restrictions, and restrictions placed on the open exchange of some commercial germplasm between breeders. The large size of most genebank collections, as well as constraints surrounding the availability and reliability of accurate germplasm passport data and physical or genetic characterization of the accessions in collections, limits germplasm utilization by plant breeders. To overcome these constraints, core collections, defined as a representative subset of the total germplasm collection, have gained popularity. Core collections aim to increase germplasm utilization by containing highly characterized germplasm that attempts to capture the majority of the variation in a whole collection. With the recent availability of many new genetic tools, the potential to unlock the value of these resources can now be realized. The Commonwealth Scientific and Industrial Research Organisation (CSIRO) cotton breeding program supplies 100% of the cotton cultivars grown in Australia. The program is reliant on the use of plant genetic resources for the development of improved cotton varieties to address emerging challenges in pest and disease resistance as well as the global changes occurring in the climate. Currently, the CSIRO germplasm collection is actively maintained but underutilized by plant breeders. This review presents an overview of the Australian cotton germplasm resources and discusses the appropriateness of a core collection for cotton breeding programs.

Genetic diversity among genotypes of Uncaria guianensis (Aubl.) J.F. Gmel. maintained in an in vitro germplasm bank

Phytotherapeutic preparations from Uncaria guianensis (Aubl.) J.F. Gmel. (Rubiaceae) are marketed worldwide and are mainly used for their anti-inflammatory activity. The species has not yet been domesticated and is threatened by deforestation and overexploitation. It is, therefore, important to preserve and manage this genetic resource in germplasm banks, so that the extractive provision of plant material can be replaced by cultivated production. The aim of this study was to evaluate the genetic diversity among 20 genotypes maintained under in vitro conditions using 9 primers start codon targeted (SCoT) polymorphism, and to determine the concentrations of the pentacyclic oxindole alkaloids (POAs); mitraphylline and isomitraphylline in methanolic extracts by high-performance liquid chromatography (HPLC). Plantlets were cultivated on woody plant medium supplemented with 20 g.L^-1 sucrose and 4.4 μM benzylaminopurine and incubated under a 16 h photoperiod for 45 days. SCoT analysis separated the genotypes into four divergent clusters and confirmed significant genetic diversity with up to 70% dissimilarity. Moreover, HPLC revealed considerable chemical variability and allowed the separation of the tested genotypes into high, medium and low producers of mitraphylline/isomitraphylline. Genotypes with the highest concentrations of POAs originated from the state of Acre and Amapá, while those with the lowest levels were from the state of Pará. The results demonstrate that the genetic diversity within the in vitro germplasm bank is sufficient to support breeding studies, selection of elite genotypes and the large-scale multiplication of plants that could serve as feedstock for the industrial-scale production of phytomedicines.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03016-y.

Sperm Repository for a Breeding Program of the Eastern Oyster Crassostrea virginica: Sample Collection, Processing, Cryopreservation, and Data Management Plan

Simple Summary

The Eastern oyster Crassostrea virginica is one of the most important fishery and aquaculture species in the USA and is a keystone species for coastal reefs. A breeding program was initiated in 2019 to support the fast-growing aquaculture industry for this species in the Gulf of Mexico. Oysters from wild populations in embayment along the U.S. Gulf of Mexico coast were used as broodstock for the program to maximize genetic diversity. A sperm repository of the broodstock, including a total of 102 male oysters from the 17 collection sites, was established to support the breeding project. Sperm collection was accomplished by strip spawn, and fresh sperm production, motility, and fertility were recorded for quality analysis. Cryopreserved sperm samples were sorted, labelled, archived, and stored in liquid nitrogen for future use. Post-thaw motility and plasm membrane integrity were recorded as post-thaw quality parameters. Overall, this study demonstrated sperm sample collection, processing, cryopreservation, and a data management plan involved in the establishment of the sperm repository. The streamlined procedure can serve as a template for construction of oyster germplasm repositories for breeding programs.

Abstract

The Eastern oyster Crassostrea virginica (Family Ostreidae) is one of the most important fishery and aquaculture species in the U.S. and is a keystone species for coastal reefs. A breeding program was initiated in 2019 to support the fast-growing aquaculture industry culturing this species in the Gulf of Mexico. Oysters from 17 wild populations in embayment along the U.S. Gulf of Mexico coast from southwest Florida to the Matagorda Bay, Texas were used as broodstock for the program to maximize genetic diversity in the base population. A sperm repository of the broodstock was established to support the breeding project. The goal of this study was to demonstrate the sperm sample collection, processing, cryopreservation, and the data management plan involved in the establishment of a sperm germplasm repository of base populations. The supporting objectives were to: (1) develop a data management plan for the sperm repository; (2) streamline the procedure for sample collection, processing, and cryopreservation; (3) incorporate sperm quality analysis into the procedure, and (4) archive the cryopreserved samples as a repository for future use in the breeding program. This sperm repository included a total of 102 male oysters from the 17 collection sites (six oysters per site). A data management plan was developed with six categories, including sample collection, phenotype, fresh sperm, genotype, cryopreservation, and post-thaw sperm, as guide for data collection. Sperm collection was accomplished by strip spawn, and fresh sperm production, motility, and fertility were recorded for quality analysis. Cryopreserved sperm samples were sorted, labelled, archived, and stored in liquid nitrogen for future use. Post-thaw motility (1–30%) and plasm membrane integrity (15.34–70.36%) were recorded as post-thaw quality parameters. Overall, this study demonstrated a streamlined procedure of oyster sperm collection, processing, and cryopreservation for establishing a sperm repository that can serve as a template for construction of oyster germplasm repositories for breeding programs.

Genetic Diversity and Environmental Influence on Growth and Yield Parameters of Bambara Groundnut

Bambara groundnut (BGN) is a drought-tolerant crop majorly cultivated in sub-Saharan Africa. Due to a lack of extensive research, marginalization, lack of awareness, and lack of available fund among others, this crop's improvement has been limited. The development of this crop depends on evaluation and selection of unique and stable breeding lines in different environments. This study aims to estimate genetic diversity using morphological traits at different locations in 95 accessions of BGN collected from the Genebank of the International Institute of Tropical Agriculture (IITA), Ibadan. The experiment was carried out in three replicates at IITA experimental sites in two agroecological zones in Ibadan (7°40'19.62″ N, 3°91'73.13″ E) and Ikenne (6°51'00.873″ N, 3°41'48.528″ E) using a randomized complete block design. Ten vegetative growth traits and eight yield traits were scored. The data was subjected to ANOVA, PCA, correlation, and cluster analysis. Estimations of genetic parameters and broad sense heritability were carried out on the traits. ANOVA revealed significant variation in each trait except for days to emergence. Significant variation was also observed for accession and location interactions (genotype x environment interactions) for plant height, leaf length, leaf width, chlorophyll content, number of petioles, germination count, number of pods, number of seeds, seed length, seed width, and yield. PC1 and PC2 show 42.3% of the total variations observed by the PC, with seed thickness contributing more to PC1 and the number of seeds contributing more to PC2. Cluster analysis categorized the accessions into four distinct groups. The number of pods had the highest genotypic coefficient of variation of 32.55% and the phenotypic coefficient of variation of 97.61%, while seed length (0.63), seed width (0.54), and seed thickness (0.58) have high heritability values. The genetic advance was highest in yield (76.15%) and lowest in days to 50% germination (0.21%). This study can be used to predict appropriate agroecological zones for the planting of BGN while the knowledge of the diversity of the accessions based on the traits could serve a guide in selecting the best trait for the improvement of the crop.

Tapping Diversity From the Wild: From Sampling to Implementation

The diversity observed among crop wild relatives (CWRs) and their ability to flourish in unfavorable and harsh environments have drawn the attention of plant scientists and breeders for many decades. However, it is also recognized that the benefit gained from using CWRs in breeding is a potential rose between thorns of detrimental genetic variation that is linked to the trait of interest. Despite the increased interest in CWRs, little attention was given so far to the statistical, analytical, and technical considerations that should guide the sampling design, the germplasm characterization, and later its implementation in breeding. Here, we review the entire process of sampling and identifying beneficial genetic variation in CWRs and the challenge of using it in breeding. The ability to detect beneficial genetic variation in CWRs is strongly affected by the sampling design which should be adjusted to the spatial and temporal variation of the target species, the trait of interest, and the analytical approach used. Moreover, linkage disequilibrium is a key factor that constrains the resolution of searching for beneficial alleles along the genome, and later, the ability to deplete linked deleterious genetic variation as a consequence of genetic drag. We also discuss how technological advances in genomics, phenomics, biotechnology, and data science can improve the ability to identify beneficial genetic variation in CWRs and to exploit it in strive for higher-yielding and sustainable crops.

Maize lethal necrosis (MLN): Efforts toward containing the spread and impact of a devastating transboundary disease in sub-Saharan Africa

Maize lethal necrosis (MLN), a complex viral disease, emerged as a serious threat to maize production and the livelihoods of smallholders in eastern Africa since 2011, primarily due to the introduction of maize chlorotic mottle virus (MCMV). The International Maize and Wheat Improvement Center (CIMMYT), in close partnership with national and international partners, implemented a multi-disciplinary and multi-institutional strategy to curb the spread of MLN in sub-Saharan Africa, and mitigate the impact of the disease. The strategy revolved around a) intensive germplasm screening and fast-tracked development and deployment of MLN-tolerant/resistant maize hybrids in Africa-adapted genetic backgrounds; b) optimizing the diagnostic protocols for MLN-causing viruses, especially MCMV, and capacity building of relevant public and private sector institutions on MLN diagnostics and management; c) MLN monitoring and surveillance across sub-Saharan Africa in collaboration with national plant protection organizations (NPPOs); d) partnership with the private seed sector for production and exchange of MLN pathogen-free commercial maize seed; and e) awareness creation among relevant stakeholders about MLN management, including engagement with policy makers. The review concludes by highlighting the need to keep continuous vigil against MLN-causing viruses, and preventing any further spread of the disease to the major maize-growing countries that have not yet reported MLN in sub-Saharan Africa.