Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles

Abstract Background Many highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions. Results Each marker was mapped with high confidence (e-30) to a single genomic location using BLASTN against tomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 ± 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles. Conclusion Of the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive identification of introgressed genes within crop species such as S. lycopersicum will help inform conservation and utilization of crop germplasm diversity, for example, facilitating the purging of undesirable linkage drag or the exploitation of novel, favorable alleles.</p

Evaluation of tomato accessions for flavour and flavour-contributing components

Flavour is one of the most highly demanded consumer traits of tomato at present; poor flavour is one of the most commonly heard complaints associated with modern varieties of tomato. In order to combine flavour with other desirable fruit traits in improved cultivars, it is important to determine how much variability exists in the crucial compounds that contribute most to flavour. The objective of the present study was to determine the variability of flavour-contributing components including total soluble solids (TSS) and total titratable acids (TTA) among other subjective traits related to flavour in a core collection of tomato accessions. The core collection was comprised of 173 tomato accessions with a wide genetic background from the United States Department of Agriculture (USDA), Agricultural Research Services (ARS) Plant Genetic Resources Unit repository. The TTA varied from 0.20 to 0.64%, whereas the TSS ranged from 3.4 to 9.0%, indicating the availability of broad variation for these traits. Rinon (PI 118783), Turrialba, Purple Calabash and LA2102 were among the high TTA (>0.45%) containing accessions, whereas those with high TSS (>7.0%) were AVRDC#6, Sponzillo and LA2102. A positive correlation of overall flavour with TTA (r=0.33; P<0.05) and TSS (r=0.37; P<0.05) indicated that these two components play an important role in determining the overall flavour in tomato. Subjectively measured other traits including fruity odour and fruity flavour had positive correlations with overall flavour. Overall flavour is discussed in the context of other traits including fruit firmness. Information obtained from this study may be useful for tomato breeders aiming to improve tomato flavou

Molecular Genetic Diversity after Reciprocal Recurrent Selection in BSSS and BSCB1 Maize Populations

Iowa Stiff Stalk Synthetic (BSSS) and Iowa Corn Borer Synthetic #1 (BSCB1) are undergoing reciprocal recurrent selection as part of Iowa\u27s Federal-State maize (Zea mays L.) breeding program. This study focused on molecular genetic variation in BSSS(R) and BSCBI(R) cycle 0 (CO) and cycle 12 (C12) populations, as well as the inbred progenitor lines (P) used to synthesize BSSS and BSCB1. The objectives were to quantify amounts of genetic variation within populations, to estimate what proportion remained after selection, and to compare genetic diversities between BSSS and BSCB1 populations. Genotypic data for 82 restriction fragment length polymorphism (RFLP) loci were collected from 100 randomly sampled individuals from each CO and C12 population, 16 BSSS(R) progenitors, and 12 BSCBI(R) progenitors. Progenitor lines were highly homozygous as expected. No single progenitor made excessive genetic contributions to CO or C12. The BSSS and BSCB1 progenitor populations were initially genetically similar (Nei\u27s genetic distance = 0.07). After 12 cycles of selection, they substantially diverged (Nei\u27s distance = 0.66). Gene diversity (expected heterozygosity under random mating) across progenitor populations was very broad (mean gene diversity = 0.6) and remained at that level to C12. Within both populations, the polymorphism level decreased from about 99 to 75%, and gene diversity decreased from about 0.6 to 0.3 between P and C12. The mean number of alleles per locus dropped from about four to less than three. Assuming an effective population size as the mean number of selected S1 lines over 12 cycles, the observed loss of variation was consistent with theoretical expectations resulting from genetic drift of neutral alleles

SSR Variation in Important U.S. Maize Inbred Lines

Historically important public inbred lines continue to play an important role in maize (Zea maysL.) improvement in many different breeding programs. Their continued use means they have undergone numerous seed increases in diverse programs since their original release. Our objective was to estimate the level of genetic diversity among and within inbred lines from different sources using SSR markers. We sampled six inbred lines (B73, CM105, Mo17, Oh43, W153R, and Wf9) obtained from 14 sources (breeding programs). The data were analyzed by analysis of molecular variance (AMOVA), genetic diversity statistics, and genetic distance (Dice\u27s coefficient). Of the total variation observed in gene frequency, 87.8% was found among inbred lines, 7.6% among sources within inbred lines, and 4.6% within sources. Genotypes of identically named inbred lines from eight different sources differed slightly on the basis of 44 SSR loci. The mean genetic similarity between sources of the same inbred was greater than 85%. It can be concluded that although more diversity exists among these six inbred lines than within them, a small but significant amount of variation exists among seed sources within inbreds. This variation may have arisen through differences in seed maintenance, since we found no evidence to suggest high mutation rates or extensive outcrossing. The small but statistically significant level of variation raises concerns in germplasm conservation, mapping studies, marker development, and long-term recombinant inbred line development, especially when high resolution is desired

AlleleCoder: a PERL script for coding co-dominant polymorphism data for PCA

A useful biological interpretation of diploid heterozygotes is in terms of the dose of the common allele (0, 1 or 2 copies). We have developed a PERL script that converts FASTA files into coded spreadsheets suitable for principal component analysis. In combination with R and R Commander, two- and three-dimensional plots can be generated for visualizing genetic relationships. Such plots are useful for characterizing plant genetic resources. This method nicely illustrated the spectrum of genetic diversity in tomato landraces and the varieties categorized according to human-mediated dispersa

Distributions, conservation status, and abiotic stress tolerance potential of wild cucurbits (Cucurbita L.)

Societal Impact Statement Crop wild relatives—wild species closely related to cultivated plants—are valuable genetic resources for crop improvement, but gaps in knowledge constrain their conservation and limit their further use. We develop new information on the distributions, potential breeding value, and conservation status of the 16 known wild relatives of cultivated pumpkins, squashes, zucchini, and gourds (Cucurbita L.). The taxa occur from the central USA to Central America, plus two South American species, with the greatest richness in central Mexico and the western borderlands between Mexico and the USA. We determine the majority of species are of medium priority for conservation, both with regard to collecting for ex situ maintenance, and for enhanced habitat protection. Summary Crop wild relatives are valuable genetic resources for crop improvement. Knowledge gaps, including with regard to taxonomy, distributions, and characterization for traits of interest constrain their use in plant breeding. These deficiencies also affect conservation planning, both with regard to in situ habitat protection, and further collection of novel diversity for ex situ maintenance. Here we model the potential ranges of all 16 known wild cucurbit taxa (Cucurbita L.), use ecogeographic information to infer their potential adaptations to abiotic stresses, and assess their ex situ and in situ conservation status. The taxa occur from the central USA to Central America, plus two South American species. Predicted taxon richness was highest in central Mexico and in the western borderlands between Mexico and the USA. We find substantial ecogeographic variation both across taxa and among populations within taxa, with regard to low temperatures, high and low precipitation, and other adaptations of potential interest for crop breeding. We categorize 13 of the taxa medium priority for further conservation as a combination of the ex situ and in situ assessments, two low priority, and one sufficiently conserved. Further action across the distributions of the taxa, with emphasis on taxonomic richness hotspots, is needed to comprehensively conserve wild Cucurbita populations

The evolutionary history of wild, domesticated, and feral Brassica oleracea (Brassicaceae)

Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using newly generated RNA-seq data for a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species can revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions

Genotyping by sequencing for SNP marker development in onion

Onion (Allium cepa) is not highly tractable for development of molecular markers due to its large (16 gigabases per 1C) nuclear genome. Single nucleotide polymorphisms (SNPs) are useful for genetic characterization and marker-aided selection of onion because of codominance and common occurrence in elite germplasm. We completed genotyping by sequencing (GBS) to identify SNPs in onion using 46 F2 plants, parents of the F2 plants (Ailsa Craig 43 and Brigham Yellow Globe 15-23), two doubled haploid (DH) lines (DH2107 and DH2110), and plants from 94 accessions in the USDA National Plant Germplasm System (NPGS). SNPs were called using the TASSEL 3.0 Universal Network Enabled Analysis (UNEAK) bioinformatics pipeline. Sequences from the F2 and DH plants were used to construct a pseudo-reference genome against which genotypes from all accessions were scored. Quality filters were used to identify a set of 284 high quality SNPs, which were placed onto an existing genetic map for the F2 family. Accessions showed a moderate level of diversity (mean He = 0.341) and evidence of inbreeding (mean F = 0.592). GBS is promising for SNP discovery in onion, although lack of a reference genome required extensive custom scripts for bioinformatics analyses to identify high quality markers.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Molecular Genetic Diversity after Reciprocal Recurrent Selection in BSSS and BSCB1 Maize Populations

Iowa Stiff Stalk Synthetic (BSSS) and Iowa Corn Borer Synthetic #1 (BSCB1) are undergoing reciprocal recurrent selection as part of Iowa's Federal-State maize (Zea mays L.) breeding program. This study focused on molecular genetic variation in BSSS(R) and BSCBI(R) cycle 0 (CO) and cycle 12 (C12) populations, as well as the inbred progenitor lines (P) used to synthesize BSSS and BSCB1. The objectives were to quantify amounts of genetic variation within populations, to estimate what proportion remained after selection, and to compare genetic diversities between BSSS and BSCB1 populations. Genotypic data for 82 restriction fragment length polymorphism (RFLP) loci were collected from 100 randomly sampled individuals from each CO and C12 population, 16 BSSS(R) progenitors, and 12 BSCBI(R) progenitors. Progenitor lines were highly homozygous as expected. No single progenitor made excessive genetic contributions to CO or C12. The BSSS and BSCB1 progenitor populations were initially genetically similar (Nei's genetic distance = 0.07). After 12 cycles of selection, they substantially diverged (Nei's distance = 0.66). Gene diversity (expected heterozygosity under random mating) across progenitor populations was very broad (mean gene diversity = 0.6) and remained at that level to C12. Within both populations, the polymorphism level decreased from about 99 to 75%, and gene diversity decreased from about 0.6 to 0.3 between P and C12. The mean number of alleles per locus dropped from about four to less than three. Assuming an effective population size as the mean number of selected S1 lines over 12 cycles, the observed loss of variation was consistent with theoretical expectations resulting from genetic drift of neutral alleles.This article is published as Labate, Joanne A., Kendall R. Lamkey, Michael Lee, and Wendy L. Woodman. "Molecular genetic diversity after reciprocal recurrent selection in BSSS and BSCB1 maize populations." Crop Science 37, no. 2 (1997): 416-423. doi: 10.2135/cropsci1997.0011183X003700020018x. Posted with permission.</p

SSR Variation in Important U.S. Maize Inbred Lines

Historically important public inbred lines continue to play an important role in maize (Zea maysL.) improvement in many different breeding programs. Their continued use means they have undergone numerous seed increases in diverse programs since their original release. Our objective was to estimate the level of genetic diversity among and within inbred lines from different sources using SSR markers. We sampled six inbred lines (B73, CM105, Mo17, Oh43, W153R, and Wf9) obtained from 14 sources (breeding programs). The data were analyzed by analysis of molecular variance (AMOVA), genetic diversity statistics, and genetic distance (Dice's coefficient). Of the total variation observed in gene frequency, 87.8% was found among inbred lines, 7.6% among sources within inbred lines, and 4.6% within sources. Genotypes of identically named inbred lines from eight different sources differed slightly on the basis of 44 SSR loci. The mean genetic similarity between sources of the same inbred was greater than 85%. It can be concluded that although more diversity exists among these six inbred lines than within them, a small but significant amount of variation exists among seed sources within inbreds. This variation may have arisen through differences in seed maintenance, since we found no evidence to suggest high mutation rates or extensive outcrossing. The small but statistically significant level of variation raises concerns in germplasm conservation, mapping studies, marker development, and long-term recombinant inbred line development, especially when high resolution is desired.This article is published as Gethi, James G., Joanne A. Labate, Kendall R. Lamkey, Margaret E. Smith, and Stephen Kresovich. "SSR variation in important US maize inbred lines." Crop science 42, no. 3 (2002): 951-957. doi: 10.2135/cropsci2002.9510. Posted with permission.</p