Population structure, relatedness and ploidy levels in an apple gene bank revealed through genotyping-by-sequencing

Comparing Apples and Oranges: Advances in Disease Resistance Breeding of Woody Perennial Fruit Crops

Apple and citrus are perennial tree fruit crops that are vital for nutritional security and agricultural economy and to achieve the Sustainable Development Goals of the United Nations. Apple scab and fire blight, along with Huanglongbing, canker, and tristeza virus, stand out as their most notorious diseases and annually destabilize fruit supply. An environmentally sound approach to managing these diseases is improving tree resistance through breeding and biotechnology. Perennial fruit tree germplasm collections are distributed globally and offer untapped potential as sources of resistance. However, long juvenility, specific pollination and flowering habits, and extensive outcrossing hinder apple and citrus breeding. Advances in breeding approaches include trans- and cis-genesis, genome editing, and rapid-cycle breeding, which, in addition to conventional crossbreeding, can all facilitate accelerated integration of resistance into elite germplasm. In addition, the global pool of available sources of resistance can be characterized by the existing genetic mapping and gene expression studies for accurate discovery of associated loci, genes, and markers to efficiently include these sources in breeding efforts. We discuss and propose a multitude of approaches to overcome the challenges of breeding for resistance in woody perennials and outline a technical path to reduce the time required for the ultimate deployment of disease-resistant cultivars.

Why we thrive beneath a northern sky - genomic signals of selection in apple for adaptation to northern Sweden

Good understanding of the genomic regions underlying adaptation of apple to boreal climates is needed to facilitate efficient breeding of locally adapted apple cultivars. Proper infrastructure for phenotyping and evaluation is essential for identification of traits responsible for adaptation, and dissection of their genetic composition. However, such infrastructure is costly and currently not available for the boreal zone of northern Sweden. Therefore, we used historical pomological data on climate adaptation of 59 apple cultivars and whole genome sequencing to identify genomic regions that have undergone historical selection among apple cultivars recommended for cultivation in northern Sweden. We found the apple collection to be composed of two ancestral groups that are largely concordant with the grouping into 'hardy' and 'not hardy' cultivars based on the pomological literature. Using a number of genome-wide scans for signals of selection, we obtained strong evidence of positive selection at a genomic region around 29 MbHFTH1 of chromosome 1 among apple cultivars in the 'hardy' group. Using phased genotypic data from the 20 K apple Infinium® SNP array, we identified haplotypes associated with the two cultivar groups and traced transmission of these haplotypes through the pedigrees of some apple cultivars. This demonstrates that historical data from pomological literature can be analyzed by population genomic approaches as a step towards revealing the genomic control of a key property for a horticultural niche market. Such knowledge is needed to facilitate efficient breeding strategies for development of locally adapted apple cultivars in the future. The current study illustrates the response to a very strong selective pressure imposed on tree crops by climatic factors, and the importance of genetic research on this topic and feasibility of breeding efforts in the light of the ongoing climate change.

Genetic diversity analysis of big-bracted dogwood (Cornus florida and C. kousa) cultivars, interspecific hybrids, and wild-collected accessions using RADseq

Big-bracted dogwoods are popular ornamental trees known for their beautiful spring blooms with showy bracts and four-season appeal. The two most widely grown species are Cornus florida and Cornus kousa, native to Eastern North America and East Asia. Despite their horticultural prominence, there is little information available regarding genetic diversity, population structure, relatedness, and subspecies origins of dogwood cultivars. In this study, 313 cultivars, wild-collected plants, and Rutgers University breeding selections, focusing on C. florida, C. kousa, and interspecific hybrids, were genotyped using restriction-site associated DNA sequencing (RADseq) generating thousands of single nucleotide polymorphism (SNP) and insertion deletion (Indel) markers. The research results showed high genetic diversity among C. florida and C. kousa wild-collected plants and cultivars. For C. florida, pink-bracted plants formed a distinct clade from those with white-bracts with the Mexican C. florida ssp. urbiniana forming an outgroup. For C. kousa, Chinese-collected plants (ssp. chinensis) were a distinct subspecies with clear separation from Japanese and Korean accessions (ssp. kousa) and cultivars were designated as ssp. chinensis, ssp. kousa, or ssp. hybrid. Using this information, a Kompetitive allele specific PCR (KASP) assay genotyping panel was designed to determine C. kousa trees' subspecies makeup. Results revealed many cases of genetically identical cultivars being sold under different names, especially for pink-bracted cultivars of both species. Additionally, reported parent-progeny relationships were evaluated and either validated or discredited. Finally, the hybrid germplasm analysis validated pedigrees of interspecific F1 hybrids and found many of the recent Rutgers breeding selections contain small regions of pacific dogwood (C. nuttallii) DNA introgressed into C. kousa backgrounds. This diversity study elucidates origins, diversity, and relationships of a large population of big-bracted dogwoods. The results can inform plant breeders, arboreta, and the ornamental plant industry, as most modern cultivars and popular historic cultivars are represented.

Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD

Microsatellite markers are widely used in population genetics and breeding. Despite the economic significance of yams in developing countries, there is a paucity of microsatellite markers, and as of now, no comprehensive microsatellite marker database exists. In this study, we conducted genome-wide microsatellite marker development across four yam species, identified cross-species transferable markers, and designed an easy-to-use web portal for the yam researchers. The screening of Dioscorea alata, Dioscorea rotundata, Dioscorea dumetorum, and Dioscorea zingiberensis genomes resulted in 318,713, 322,501, 307,040, and 253,856 microsatellites, respectively. Mono-, di-, and tri-nucleotides were the most important types of repeats in the different species, and a total of 864,128 primer pairs were designed. Furthermore, we identified 1170 cross-species transferable microsatellite markers. Among them, 17 out of 18 randomly selected were experimentally validated with good discriminatory power, regardless of the species and ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at https://y2md.ucad.sn/. Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. This study represents the first comprehensive microsatellite marker mining across several yam species and will contribute to advancing yam genetic research and marker-assisted breeding. The released user-friendly database constitutes a valuable platform for yam researchers.

RP, R. L. R. Population structure and genetic diversity characterization of soybean for seed longevity

Seed longevity is an important trait in the context of germplasm conservation and economics of seed production. The identification of populations with high level of genetic variability for seed longevity and associated traits will become a valuable resource for superior alleles for seed longevity. In this study, Genotyping-by-sequencing (GBS)-single nucleotide polymorphism (SNP) approach, simple sequence repeats (SSR) markers and agro-morphological traits have been explored to investigate the diversity and population structure of assembled 96 genotypes. The GBS technique performed on 96 genotypes of soybean (Glycine max (L.) Merrill) resulted in 37,897 SNPs on sequences aligned to the reference genome sequence. The average genome coverage was 6.81X with a mapping rate of 99.56% covering the entire genome. Totally, 29,955 high quality SNPs were identified after stringent filtering and most of them were detected in non-coding regions. The 96 genotypes were phenotyped for eight quantitative and ten qualitative traits by growing in field by following augmented design. The STRUCTURE (Bayesian-model based algorithm), UPGMA (Un-weighed Pair Group Method with Arithmetic mean) and principal component analysis (PCA) approaches using SSR, SNP as well as quantitative and qualitative traits revealed population structure and diversity in assembled population. The Bayesian-model based STRUCTURE using SNP markers could effectively identify clusters with higher seed longevity associated with seed coat colour and size which were subsequently validated by UPGMA and PCA based on SSR and agro-morphological traits. The results of STRUCTURE, PCA and UPGMA cluster analysis showed high degree of similarity and provided complementary data that helped to identify genotypes with higher longevity. Six black colour genotypes, viz., Local black soybean, Kalitur, ACC Nos. 39, 109, 101 and 37 showed higher seed longevity during accelerated ageing. Higher coefficient of variability observed for plant height, number of pods per plant, seed yield per plant, 100 seed weight and seed longevity confirms the diversity in assembled population and its suitability for quantitative trait loci (QTL) mapping.

Genetic Diversity and Pedigree Analysis of Red Currant Germplasm

This represents the first report on the genetic diversity of red currant germplasm collections based on genotyping-by-sequencing (GBS) data. Genotypes of 75 individuals of different origin were assessed in more than 7.5K genome positions. Multidimensional scaling (MDS) analysis has been performed. There are five accessions that are significantly isolated from each other and from the rest of the analyzed cultivars. F₁ offspring of R. petraeum Wulf (Rote Hollandische) and Gondouin, as well as Rote Spatlese (F₂ of R. petraeum and F₂ of R. multiflorum Kit.), are the most genetically isolated on the MDS plot. Ribes multiflorum is closer to the rest of cultivars than the three abovementioned accessions. Purpurnaya cultivar (F₁ of Rote Spatlese) is located between Rote Hollandische and R. multiflorum. Other genotypes, mostly represented by varieties having several species in a pedigree, occupied the rest of MDS plot relatively evenly. Descendants of R. multiflorum have been placed in the left part of MDS plot, which underlines their genetic diversity from other accessions. White- and pink-fruited cultivars were clustered together, underlining genetic relatedness. Admixture analysis of GBS data reveals six clusters (K = 6). Presumably, clustering reflects relatedness to R. petraeum, R. rubrum, R. vulgare var macrocarpum, R. multiflorum, R. vulgare, and Jonker van Tets. Based on genotyping data, F₁ offspring of R. warscewiczs Jancz (cultivar Viksne), R. altissimum Turcz (Cirald), and R. palczewskii (Jancz.) Pojark (Skorospelaya) have not exhibited strict separation and were placed in a pool with other varieties. This supports modern taxonomic classifications that do not consider R. altissimum and R. palczewskii as independent species.

A new method to reconstruct the direction of parent-offspring duo relationships using SNP array data and its demonstration on ancient and modern cultivars in the outcrossing species malus × domestica

Unordered parent-offspring (PO) relationships are an outstanding issue in pedigree reconstruction studies. Resolution of the order of these relationships would expand the results, conclusions, and usefulness of such studies; however, no such PO order resolution (POR) tests currently exist. This study describes two such tests, demonstrated using SNP array data in the outcrossing species apple (Malus × domestica) on a PO relationship of known order ("Keepsake" as a parent of "Honeycrisp") and two PO relationships previously ordered only via provenance information. The first test, POR-1, tests whether some of the extended haplotypes deduced from homozygous SNP calls from one individual in an unordered PO duo are composed of recombinant haplotypes from accurately phased SNP genotypes from the second individual. If so, the first individual would be the offspring of the second individual, otherwise the opposite relationship would be present. The second test, POR-2, does not require phased SNP genotypes and uses similar logic as the POR-1 test, albeit in a different approach. The POR-1 and POR-2 tests determined the correct relationship between "Keepsake" and "Honeycrisp". The POR-2 test confirmed "Reinette Franche" as a parent of "Nonpareil" and "Brabant Bellefleur" as a parent of "Court Pendu Plat". The latter finding conflicted with the recorded provenance information, demonstrating the need for these tests. The successful demonstration of these tests suggests they can add insights to future pedigree reconstruction studies, though caveats, like extreme inbreeding or selfing, would need to be considered where relevant.

Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS)

Olives are one of the most important fruit and woody oil trees cultivated in many parts of the world. Olive oil is a critical component of the Mediterranean diet due to its importance in heart health. Olives are believed to have been brought to the United States from the Mediterranean countries in the 18th century. Despite the increase in demand and production areas, only a few selected olive varieties are grown in most traditional or new growing regions in the US. By understanding the genetic background, new sources of genetic diversity can be incorporated into the olive breeding programs to develop regionally adapted varieties for the US market. This study aimed to explore the genetic diversity and population structure of 90 olive accessions from the USDA repository along with six popular varieties using genotyping-by-sequencing (GBS)-generated SNP markers. After quality filtering, 54,075 SNP markers were retained for the genetic diversity analysis. The average gene diversity (GD) and polymorphic information content (PIC) values of the SNPs were 0.244 and 0.206, respectively, indicating a moderate genetic diversity for the US olive germplasm evaluated in this study. The structure analysis showed that the USDA collection was distributed across seven subpopulations; 63% of the accessions were grouped into an identifiable subpopulation. The phylogenetic and principal coordinate analysis (PCoA) showed that the subpopulations did not align with the geographical origins or climatic zones. An analysis of the molecular variance revealed that the major genetic variation sources were within populations. These findings provide critical information for future olive breeding programs to select genetically distant parents and facilitate future gene identification using genome-wide association studies (GWAS) or a marker-assisted selection (MAS) to develop varieties suited to production in the US.

A Semi-Automated SNP-Based Approach for Contaminant Identification in Biparental Polyploid Populations of Tropical Forage Grasses

Artificial hybridization plays a fundamental role in plant breeding programs since it generates new genotypic combinations that can result in desirable phenotypes. Depending on the species and mode of reproduction, controlled crosses may be challenging, and contaminating individuals can be introduced accidentally. In this context, the identification of such contaminants is important to avoid compromising further selection cycles, as well as genetic and genomic studies. The main objective of this work was to propose an automated multivariate methodology for the detection and classification of putative contaminants, including apomictic clones (ACs), self-fertilized individuals, half-siblings (HSs), and full contaminants (FCs), in biparental polyploid progenies of tropical forage grasses. We established a pipeline to identify contaminants in genotyping-by-sequencing (GBS) data encoded as allele dosages of single nucleotide polymorphism (SNP) markers by integrating principal component analysis (PCA), genotypic analysis (GA) measures based on Mendelian segregation, and clustering analysis (CA). The combination of these methods allowed for the correct identification of all contaminants in all simulated progenies and the detection of putative contaminants in three real progenies of tropical forage grasses, providing an easy and promising methodology for the identification of contaminants in biparental progenies of tetraploid and hexaploid species. The proposed pipeline was made available through the polyCID Shiny app and can be easily coupled with traditional genetic approaches, such as linkage map construction, thereby increasing the efficiency of breeding programs.

The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry

Pedigree information is of fundamental importance in breeding programs and related genetics efforts. However, many individuals have unknown pedigrees. While methods to identify and confirm direct parent-offspring relationships are routine, those for other types of close relationships have yet to be effectively and widely implemented with plants, due to complications such as asexual propagation and extensive inbreeding. The objective of this study was to develop and demonstrate methods that support complex pedigree reconstruction via the total length of identical by state haplotypes (referred to in this study as "summed potential lengths of shared haplotypes", SPLoSH). A custom Python script, HapShared, was developed to generate SPLoSH data in apple and sweet cherry. HapShared was used to establish empirical distributions of SPLoSH data for known relationships in these crops. These distributions were then used to estimate previously unknown relationships. Case studies in each crop demonstrated various pedigree reconstruction scenarios using SPLoSH data. For cherry, a full-sib relationship was deduced for 'Emperor Francis, and 'Schmidt', a half-sib relationship for 'Van' and 'Windsor', and the paternal grandparents of 'Stella' were confirmed. For apple, 29 cultivars were found to share an unknown parent, the pedigree of the unknown parent of 'Cox's Pomona' was reconstructed, and 'Fameuse' was deduced to be a likely grandparent of 'McIntosh'. Key genetic resources that enabled this empirical study were large genome-wide SNP array datasets, integrated genetic maps, and previously identified pedigree relationships. Crops with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction.

Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.

Genomic consequences of apple improvement

The apple (Malus domestica) is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years. Here, we genetically characterise over 1000 apple accessions from the United States Department of Agriculture (USDA) germplasm collection using over 30,000 single-nucleotide polymorphisms (SNPs). We confirm the close genetic relationship between modern apple cultivars and their primary progenitor species, Malus sieversii from Central Asia, and find that cider apples derive more of their ancestry from the European crabapple, Malus sylvestris, than do dessert apples. We determine that most of the USDA collection is a large complex pedigree: over half of the collection is interconnected by a series of first-degree relationships. In addition, 15% of the accessions have a first-degree relationship with one of the top 8 cultivars produced in the USA. With the exception of 'Honeycrisp', the top 8 cultivars are interconnected to each other via pedigree relationships. The cultivars 'Golden Delicious' and 'Red Delicious' were found to have over 60 first-degree relatives, consistent with their repeated use by apple breeders. We detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased firmness. Our results suggest that Americans are eating apples largely from a single family tree and that the apple's future improvement will benefit from increased exploitation of its tremendous natural genetic diversity.

Development of a minimal KASP marker panel for distinguishing genotypes in apple collections

Accurate identification of named accessions in germplasm collections is extremely important, especially for vegetatively propagated crops which are expensive to maintain. Thus, an inexpensive, reliable, and rapid genotyping method is essential because it avoids the need for laborious and time-consuming morphological comparisons. Single Nucleotide Polymorphism (SNP) marker panels containing large numbers of SNPs have been developed for many crop species, but such panels are much too large for basic cultivar identification. Here, we have identified a minimum set of SNP markers sufficient to distinguish apple cultivars held in the English and Welsh national collections providing a cheaper and automatable alternative to the markers currently used by the community. We show that SNP genotyping with a small set of well selected markers is equally efficient as microsatellites for the identification of apple cultivars and has the added advantage of automation and reduced cost when screening large numbers of samples.

Comparison Between Core Set Selection Methods Using Different Illumina Marker Platforms: A Case Study of Assessment of Diversity in Wheat

Collections of plant genetic resources stored in genebanks are an important source of genetic diversity for improvement in plant breeding programs and for conservation of natural variation. The establishment of reduced representative collections from a large set of genotypes is a valuable tool that provides cost-effective access to the diversity present in the whole set. Software like Core Hunter 3 is available to generate high quality core sets. In addition, general clustering approaches, e.g., k-medoids, are available to subdivide a large data set into small groups with maximum genetic diversity between groups. Illumina genotyping platforms are a very efficient tool for the assessment of genetic diversity of plant genetic resources. The accumulation of genotyping data over time using commercial genotyping platforms raises the question of how such huge amount of information can be efficiently used for creating core collections. In the present study, after developing a 15K wheat Infinium array with 12,908 SNPs and genotyping a set of 479 hexaploid winter wheat lines (Triticum aestivum), a larger data set was created by merging 411 lines previously genotyped with the 90K iSelect array. Overlaying the markers from the 15K and 90K arrays enabled the identification of a common set of 12,806 markers, suggesting that the 15K array is a valuable and cost-effective resource for plant breeding programs. Finally, we selected genetically diverse core sets out of these 890 wheat genotypes derived from five collections based on the common markers from the 15K and 90K SNP arrays. Two different approaches, k-medoids and Core Hunter 3 were compared,and k-medoids was identified as an efficient method for selecting small core sets out of a large collection of genotypes while retaining the genetic diversity of the original population.

Genome-Wide Association Studies in Apple Reveal Loci for Aroma Volatiles, Sugar Composition, and Harvest Date

Understanding the genetic architecture of fruit quality traits is crucial to target breeding of apple ( L.) cultivars. We linked genotype and phenotype information by combining genotyping-by-sequencing (GBS) generated single nucleotide polymorphism (SNP) markers with fruit flavor volatile data, sugar and acid content, and historical trait data from a gene bank collection. Using gas chromatography-mass spectrometry (GC-MS) analysis of apple juice samples, we identified 49 fruit volatile organic compounds (VOCs). We found a very variable content of VOCs, especially for the esters, among 149 apple cultivars. We identified convincing associations for the acetate esters especially butyl acetate and hexyl acetate on chromosome 2 in a region of several alcohol acyl-transferases including AAT1. For sucrose content and for fructose and sucrose in percentage of total sugars, we revealed significant SNP associations. Here, we suggest a vacuolar invertase close to significant SNPs for this association as candidate gene. Harvest date was in strong SNP association with a NAC transcription factor gene and sequencing identified two haplotypes associated with harvest date. The study shows that SNP marker characterization of a gene bank collection can be successfully combined with new and historical trait data for association studies. Suggested candidate genes may contribute to an improved understanding of the genetic basis for important traits and simultaneously provide tools for targeted breeding using marker-assisted selection (MAS).

Origins of the Apple: The Role of Megafaunal Mutualism in the Domestication of Malus and Rosaceous Trees

The apple (Malus domestica [Suckow] Borkh.) is one of the most economically and culturally significant fruits in the world today, and it is grown in all temperate zones. With over a thousand landraces recognized, the modern apple provides a unique case study for understanding plant evolution under human cultivation. Recent genomic and archaeobotanical studies have illuminated parts of the process of domestication in the Rosaceae family. Interestingly, these data seem to suggest that rosaceous arboreal crops did not follow the same pathway toward domestication as other domesticated, especially annual, plants. Unlike in cereal crops, tree domestication appears to have been rapid and driven by hybridization. Apple domestication also calls into question the concept of centers of domestication and human intentionality. Studies of arboreal domestication also illustrate the importance of fully understanding the seed dispersal processes in the wild progenitors when studying crop origins. Large fruits in Rosaceae evolved as a seed-dispersal adaptation recruiting megafaunal mammals of the late Miocene. Genetic studies illustrate that the increase in fruit size and changes in morphology during evolution in the wild resulted from hybridization events and were selected for by large seed dispersers. Humans over the past three millennia have fixed larger-fruiting hybrids through grafting and cloning. Ultimately, the process of evolution under human cultivation parallels the natural evolution of larger fruits in the clade as an adaptive strategy, which resulted in mutualism with large mammalian seed dispersers (disperser recruitment).

Apple whole genome sequences: recent advances and new prospects

In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for "what's next" focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.