Genetic diversity and linkage disequilibrium analysis in elite sugar beet breeding lines and wild beet accessions

Beta vulgaris ssp. vulgaris chromosome 8 shows significant association with geosmin concentration in table beet

Geosmin, a degraded sesquiterpene molecule with earthy and musty odor, imbues table beet with its characteristic aroma. Geosmin is heritable and endogenously produced in table beet; its earthy aroma is sought by some consumers but deters others. Geosmin biosynthesis is catalyzed by a bifunctional geosmin synthase enzyme in diverse bacteria and fungi, but a mechanism for geosmin biosynthesis in plants has not been reported. This work employed association analysis and selective genotyping of a segregating F2:3 mapping population to seek QTL associated with geosmin concentration in table beet. GBS reads were aligned to sugar beet reference genome EL10.2, and association analysis revealed two QTL for geosmin concentration on Beta vulgaris ssp. vulgaris chromosome 8. QTL at EL10.2 positions 28,017,624 and 38,488,687 each show effect size 8.7 μg·kg-1 geosmin and explain 8.5% and 6.4% of total variation in geosmin concentration, respectively. Resolution was low due to large recombination bin size and imperfect alignment between the reference genome and mapping population, but population size and selection proportion were sufficient to detect moderate to large effect QTL. This study, the first molecular genetic mapping experiment in table beet, succeeded in finding QTL for geosmin concentration in table beet, and it provides the basis for fine mapping or candidate gene investigation of functional loci for this distinctive sensory trait.

Genomic insight into the developmental history of southern highbush blueberry populations

Interspecific hybridization is a common breeding approach for introducing novel traits and genetic diversity to breeding populations. Southern highbush blueberry (SHB) is a blueberry cultivar group that has been intensively bred over the last 60 years. Specifically, it was developed by multiple interspecific crosses between northern highbush blueberry [NHB, Vaccinium corymbosum L. (2n = 4x = 48)] and low-chill Vaccinium species to expand the geographic limits of highbush blueberry production. In this study, we genotyped polyploid blueberries, including 105 SHB, 17 NHB, and 10 rabbiteye blueberry (RE) (Vaccinium virgatum Aiton), from the accessions planted at Poplarville, Mississippi, and accessions distributed in Japan, based on the double-digest restriction site-associated DNA sequencing. The genome-wide SNP data clearly indicated that RE cultivars were genetically distinct from SHB and NHB cultivars, whereas NHB and SHB were genetically indistinguishable. The population structure results appeared to reflect the differences in the allele selection strategies that breeders used for developing germplasm adapted to local climates. The genotype data implied that there are no or very few genomic segments that were commonly introgressed from low-chill Vaccinium species to the SHB genome. Principal component analysis-based outlier detection analysis found a few loci associated with a variable that could partially differentiate NHB and SHB. These SNP loci were detected in Mb-scale haplotype blocks and may be close to the functional genes related to SHB development. Collectively, the data generated in this study suggest a polygenic adaptation of SHB to the southern climate, and may be relevant for future population-scale genome-wide analyses of blueberry.

Discovery of interesting new polymorphisms in a sugar beet (elite [Formula: see text] exotic) progeny by comparison with an elite panel

KEY MESSAGE

The comparison of QTL detection performed on an elite panel and an (elite [Formula: see text] exotic) progeny shows that introducing exotic germplasm into breeding programs can bring new interesting allelic diversity. Selection of stable varieties producing the highest amount of extractable sugar per hectare (ha), resistant to diseases, and respecting environmental criteria is undoubtedly the main target for sugar beet breeding. As sodium, potassium, and [Formula: see text]-amino nitrogen in sugar beets are the impurities that have the biggest negative impact on white sugar extraction, it is interesting to reduce their concentration in further varieties. However, domestication history and strong selection pressures have affected the genetic diversity needed to achieve this goal. In this study, quantitative trait locus (QTL) detection was performed on two populations, an (elite [Formula: see text] exotic) sugar beet progeny and an elite panel, to find potentially new interesting regions brought by the exotic accession. The three traits linked with impurities content were studied. Some QTLs were detected in both populations, the majority in the elite panel because of most statistical power. Some of the QTLs were colocated and had favorable effect in the progeny since the exotic allele was linked with a decrease in the impurity content. A few number of favorable QTLs were detected in the progeny, only. Consequently, introgressing exotic genetic material into sugar beet breeding programs can allow the incorporation of new interesting alleles.

Insights into the genetic relationships among plants of Beta section Beta using SNP markers

Using a much higher number of SNP markers and larger sample sizes than all the previous studies, we characterized the genetic relationships among wild and cultivated plants of section Beta. We analyzed the genetic variation of Beta section Beta, which includes wild taxa (Beta macrocarpa, B. patula, B. vulgaris subsp. adanensis and B. vulgaris subsp. maritima) and cultivars (fodder beet, sugar beet, garden beet, leaf beet, and swiss chards), using 9724 single nucleotide polymorphism markers. The analyses conducted at the individual level without a priori groups confirmed the strong differentiation of B. macrocarpa and B. vulgaris subsp. adanensis from the other taxa. B. vulgaris subsp. maritima showed a complex genetic structure partly following a geographical pattern, which confounded the differences between this taxon and the cultivated varieties. Cultivated varieties were structured into three main groups: garden beets, fodder and sugar beets, and leaf beets and swiss chards. The genetic structure described here will be helpful to correctly estimate linkage disequilibrium and to test for statistical associations between genetic markers and environmental variables.

Genetic diversity and association mapping in the Colombian Central Collection of Solanum tuberosum L. Andigenum group using SNPs markers

The potato (Solanum tuberosum L.) is the fourth most important crop food in the world and Colombia has one of the most important collections of potato germplasm in the world (the Colombian Central Collection-CCC). Little is known about its potential as a source of genetic diversity for molecular breeding programs. In this study, we analyzed 809 Andigenum group accessions from the CCC using 5968 SNPs to determine: 1) the genetic diversity and population structure of the Andigenum germplasm and 2) the usefulness of this collection to map qualitative traits across the potato genome. The genetic structure analysis based on principal components, cluster analyses, and Bayesian inference revealed that the CCC can be subdivided into two main groups associated with their ploidy level: Phureja (diploid) and Andigena (tetraploid). The Andigena population was more genetically diverse but less genetically substructured than the Phureja population (three vs. five subpopulations, respectively). The association mapping analysis of qualitative morphological data using 4666 SNPs showed 23 markers significantly associated with nine morphological traits. The present study showed that the CCC is a highly diverse germplasm collection genetically and phenotypically, useful to implement association mapping in order to identify genes related to traits of interest and to assist future potato genetic breeding programs.

Evaluation of LD decay and various LD-decay estimators in simulated and SNP-array data of tetraploid potato

The number of SNPs required for QTL discovery is justified by the distance at which linkage disequilibrium has decayed. Simulations and real potato SNP data showed how to estimate and interpret LD decay. The magnitude of linkage disequilibrium (LD) and its decay with genetic distance determine the resolution of association mapping, and are useful for assessing the desired numbers of SNPs on arrays. To study LD and LD decay in tetraploid potato, we simulated autotetraploid genotypes and used it to explore the dependence on: (1) the number of haplotypes in the population (the amount of genetic variation) and (2) the percentage of haplotype specific SNPs (hs-SNPs). Several estimators for short-range LD were explored, such as the average r ², median r ², and other percentiles of r ² (80, 90, and 95 %). For LD decay, we looked at LD_½,90, the distance at which the short-range LD is halved when using the 90 % percentile of r ² at short range, as estimator for LD. Simulations showed that the performance of various estimators for LD decay strongly depended on the number of haplotypes, although the real value of LD decay was not influenced very much by this number. The estimator LD_½,90 was chosen to evaluate LD decay in 537 tetraploid varieties. LD_½,90 values were 1.5 Mb for varieties released before 1945 and 0.6 Mb in varieties released after 2005. LD_½,90 values within three different subpopulations ranged from 0.7 to 0.9 Mb. LD_½,90 was 2.5 Mb for introgressed regions, indicating large haplotype blocks. In pericentromeric heterochromatin, LD decay was negligible. This study demonstrates that several related factors influencing LD decay could be disentangled, that no universal approach can be suggested, and that the estimation of LD decay has to be performed with great care and knowledge of the sampled material.

Epigenomics and bolting tolerance in sugar beet genotypes

In sugar beet (Beta vulgaris altissima), bolting tolerance is an essential agronomic trait reflecting the bolting response of genotypes after vernalization. Genes involved in induction of sugar beet bolting have now been identified, and evidence suggests that epigenetic factors are involved in their control. Indeed, the time course and amplitude of DNA methylation variations in the shoot apical meristem have been shown to be critical in inducing sugar beet bolting, and a few functional targets of DNA methylation during vernalization have been identified. However, molecular mechanisms controlling bolting tolerance levels among genotypes are still poorly understood. Here, gene expression and DNA methylation profiles were compared in shoot apical meristems of three bolting-resistant and three bolting-sensitive genotypes after vernalization. Using Cot fractionation followed by 454 sequencing of the isolated low-copy DNA, 6231 contigs were obtained that were used along with public sugar beet DNA sequences to design custom Agilent microarrays for expression (56k) and methylation (244k) analyses. A total of 169 differentially expressed genes and 111 differentially methylated regions were identified between resistant and sensitive vernalized genotypes. Fourteen sequences were both differentially expressed and differentially methylated, with a negative correlation between their methylation and expression levels. Genes involved in cold perception, phytohormone signalling, and flowering induction were over-represented and collectively represent an integrative gene network from environmental perception to bolting induction. Altogether, the data suggest that the genotype-dependent control of DNA methylation and expression of an integrative gene network participate in bolting tolerance in sugar beet, opening up perspectives for crop improvement.

Breeding patterns and cultivated beets origins by genetic diversity and linkage disequilibrium analyses

Genetic diversity in worldwide population of beets is strongly affected by the domestication history, and the comparison of linkage disequilibrium in worldwide and elite populations highlights strong selection pressure. Genetic relationships and linkage disequilibrium (LD) were evaluated in a set of 2035 worldwide beet accessions and in another of 1338 elite sugar beet lines, using 320 and 769 single nucleotide polymorphisms, respectively. The structures of the populations were analyzed using four different approaches. Within the worldwide population, three of the methods gave a very coherent picture of the population structure. Fodder beet and sugar beet accessions were grouped together, separated from garden beets and sea beets, reflecting well the origins of beet domestication. The structure of the elite panel, however, was less stable between clustering methods, which was probably because of the high level of genetic mixing in breeding programs. For the linkage disequilibrium analysis, the usual measure (r (2)) was used, and compared with others that correct for population structure and relatedness (r S (2) , r V (2) , r VS (2)). The LD as measured by r (2) persisted beyond 10 cM within the elite panel and fell below 0.1 after less than 2 cM in the worldwide population, for almost all chromosomes. With correction for relatedness, LD decreased under 0.1 by 1 cM for almost all chromosomes in both populations, except for chromosomes 3 and 9 within the elite panel. In these regions, the larger extent of LD could be explained by strong selection pressure.

Genome-wide association mapping for kernel and malting quality traits using historical European barley records

Malting quality is an important trait in breeding barley (Hordeum vulgare L.). It requires elaborate, expensive phenotyping, which involves micro-malting experiments. Although there is abundant historical information available for different cultivars in different years and trials, that historical information is not often used in genetic analyses. This study aimed to exploit historical records to assist in identifying genomic regions that affect malting and kernel quality traits in barley. This genome-wide association study utilized information on grain yield and 18 quality traits accumulated over 25 years on 174 European spring and winter barley cultivars combined with diversity array technology markers. Marker-trait associations were tested with a mixed linear model. This model took into account the genetic relatedness between cultivars based on principal components scores obtained from marker information. We detected 140 marker-trait associations. Some of these associations confirmed previously known quantitative trait loci for malting quality (on chromosomes 1H, 2H, and 5H). Other associations were reported for the first time in this study. The genetic correlations between traits are discussed in relation to the chromosomal regions associated with the different traits. This approach is expected to be particularly useful when designing strategies for multiple trait improvements.