H.J. van Eck

Genome sequence and analysis of the tuber crop potato.

Potato (Solanum tuberosum L.) is the world’s most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

A genetic map of potato (Solanum tuberosum) integrating molecular markers, including transposons, and classical markers.

A genetic map of potato (Solanum tuberosum L.) integrating molecular markers with morphological and isozyme markers was constructed using a backcross population of 67 diploid potato plants. A general method for map construction is described that differs from previous methods employed in potato and other outbreeding plants. First, separate maps for the female and male parents were constructed. The female map contained 132 markers, whereas the male map contained 138 markers. Second, on the basis of the markers in common the two integrated parental maps were combined into one with the computer programme JoinMap. This combined map consisted of 175 molecular markers, 10 morphological markers and 8 isozyme markers. Ninety-two of the molecular markers were derived from DNA sequences flanking either T-DNA inserts in potato or reintegrated maize transposable elements originating from these T-DNA constructs. Clusters of distorted segregation were found on chromosomes 1,2,8 and 11 for the male parent and chromosome 5 for both parents. The total length of the combined map is 1120 cM.

Can the QTL for late blight resistance on potato chromosome 5 be attributed to foliage maturity type

Abstract.We investigated the association between late blight resistance and foliage maturity type in potato by means of molecular markers. Two QTLs were detected for foliage resistance against Phytophthora infestans (on chromosomes 3 and 5) and one for foliage maturity type (on chromosome 5). The QTL for resistance to late blight and the QTL for foliage maturity type on chromosome 5 appeared to be mapped on indistinguishable positions. We were interested whether this genetic linkage was due to closely linked but different genes, or due to one (or more) gene(s) with pleiotropic effects. We therefore developed an approach to detect QTLs, in which resistance to late blight was adjusted for foliage maturity type. This analysis revealed the same two QTLs for resistance against P. infestans, but the effect of the locus on chromosome 5 was reduced to only half the original effect. This is a strong indication that the two indistinguishable QTLs for foliage maturity type and for late blight resistance on chromosome 5 may actually be one gene with a pleiotropic effect on both traits. However, there was still a significant effect on resistance against P. infestans on the locus on chromosome 5 after adjusting for foliage maturity type. Therefore we cannot rule out the presence of two closely linked QTLs on chromosome 5: one with a pleiotropic effect on both late blight resistance and foliage maturity type, and another with merely an effect on resistance. In addition, the two QTLs for resistance to late blight showed an important epistatic interaction, suggesting that QTLs for resistance affect each others expression.

Genetic diversity of taro, Colocasia esculenta (L.) Schott, in Southeast Asia and the Pacific

The genetic diversity of 255 taro (Colocasia esculenta) accessions from Vietnam, Thailand, Malaysia, Indonesia, the Philippines, Papua New Guinea and Vanuatu was studied using AFLPs. Three AFLP primer combinations generated a total of 465 scorable amplification products. The 255 accessions were grouped according to their country of origin, to their ploidy level (diploid or triploid) and to their habitat—cultivated or wild. Gene diversity within these groups and the genetic distance between these groups were computed. Dendrograms were constructed using UPGMA cluster analysis. In each country, the gene diversity within the groups of wild genotypes was the highest compared to the diploid and triploid cultivars groups. The highest gene diversity was observed for the wild group from Thailand (0.19), the lowest for the diploid cultivars group from Thailand (0.007). In Malaysia there was hardly any difference between the gene diversity of the cultivars and wild groups, 0.07 and 0.08, respectively. The genetic distances between the diploid cultivars groups ranges from 0.02 to 0.10, with the distance between the diploid accessions from Thailand and Malaysia being the highest. The genetic distances between the wild groups range from 0.05 to 0.07. First, a dendrogram was constructed with only the diploids cultivars from all countries. The accessions formed clusters largely according to the country from which they originated. Two major groups of clusters were revealed, one group assembling accessions from Asian countries and the other assembling accessions from the Pacific. Surprisingly, the group of diploid cultivars from Thailand clustered among the Pacific countries. Secondly, a dendrogram was constructed with diploid cultivated, triploid cultivated and wild accessions. Again the division of the accessions into an Asian and a Pacific gene pool is obvious. The presence of two gene pools for cultivated diploid taro has major implications for the breeding and conservation of germplasm.

An Online Potato Pedigree Database Resource

At the Laboratory of Plant Breeding of Wageningen University, a large amount of pedigree data on current and historic potato cultivars and progenitors has been collected over many years. The sources and reasons for collection of these data are discussed. To allow others to use this data set for their own purposes, we have created a Web-accessible interface that allows querying of these data, e.g., for the ancestry of a cultivar of interest. This Web interface was recently extended and improved to allow users to create reports and dynamically created pedigree-tree images. Availability of this resource and the options provided by the new Web interface are presented.

Identification and mapping of three flower colour loci of potato (S. tuberosum L.) by RFLP analysis.

SummaryThe inheritance of flower colour in diploid potato (2 n = 2x = 24), was found to be controlled by three unlinked loci D, F and P. To determine the allelism with previously described loci and to dissect this oligogenic trait, a set of tester clones with well-defined genotypes was developed. By backcrossing the mapping population with these tester clones it was possible to obtain monogenic segregation ratios. These were required to detect linkage with RFLP loci and, despite distorted Mendelian ratios, the inheritance and mapping of the D, F and P loci could be unambiguously determined. Locus D, involved in the biosynthesis of red anthocyanins, was mapped on chromosome 2, while locus P, involved in the production of blue anthocyanins, was mapped on chromosome 11. Locus F, involved in the flower-specific expression of gene(s) accommodated by the D and P loci, was mapped on chromosome 10. The tester clones and the map position of the D, F and P loci may be of considerable value in simplifying the genetics of anthocyanin pigmentation.

Genetics of morphological and tuber traits

Publisher Summary This chapter describes most tuber traits from a strict genetics point of view. Genetics in the strict sense simply refers to understanding the heritable basis of a trait. This can be achieved by using an experimental design that allows correlating phenotypic variation with variation at the allele or genotype level. Currently, the genotypic information is obtained with molecular marker techniques. This implies that the geneticist has the ability to tag any locus with a marker. In this way, the geneticist can offer conclusive evidence for the presence of a locus involved in heritable trait variation. More specifically, it refers to broad-sense heritability in potato, because in non-inbred species, the heritability is always the summation of additive and dominance genetic variance. Only when more recent publications have shed new light on a classical tuber trait, the added value of the new papers will be reviewed. The topics in this chapter can be subdivided into a number of classes of tuber traits. Some of these classes may overlap, but this overlap is ignored to organize a common sense order in the presentation of tuber traits. A subset of the tuber traits is only presented in the table and not discussed in the text because of lack of relevant hereditary information.

Possibilities and Challenges of the Potato Genome Sequence

This paper describes the progress that has been made since the draft genome sequence of potato has been obtained and the analyses that need to be done to make further progress. Although sequencing has become less expensive and read lengths have increased, making optimal use of the information obtained is still difficult, certainly in the tetraploid potato crop. Major challenges in potato genomics are standardized genome assembly and haplotype analysis. Sequencing methods need to be improved further to achieve precision breeding. With the current new generation sequencing technology, the focus in potato breeding will shift from phenotype improvement to genotype improvement. In this respect, it is essential to realize that different alleles of the same gene can lead to different phenotypes depending on the genetic background and that there is significant epistatic interaction between different alleles. Genome-wide association studies will gain statistical power when binary single nucleotide polymorphism (SNP) data can be replaced with multi-allelic haplotype data. Binary SNP can be distributed across the many different alleles per locus or may be haplotype-specific, and potentially tag specific alleles which clearly differ in their contribution to a certain trait value. Assembling reads from the same linkage phase proved to allow constructing sufficiently long haplotype tracts to ensure their uniqueness. Combining large phenotyping data sets with modern approaches to sequencing and haplotype analysis and proper software will allow the efficiency of potato breeding to increase.

QTL mapping in diploid potato by using selfed progenies of the cross S. tuberosum × S. chacoense

Usually, mapping studies in potato are performed with segregating populations from crosses between highly heterozygous diploid or tetraploid parents. These studies are hampered by a high level of genetic background noise due to the numerous segregating alleles, with a maximum of eight per locus. In the present study, we aimed to increase the mapping efficiency by using progenies from diploid inbred populations in which at most two alleles segregate. Selfed progenies were generated from a cross between S. tuberosum (D2; a highly heterozygous diploid) and S. chacoense (DS; a homozygous diploid clone) containing the self-incompatibility overcoming S locus inhibitor (Sli-gene). The Sli-gene enables self-pollination and the generation of selfed progenies. One F2 population was used to map several quality traits, such as tuber shape, flesh and skin color. Quantitative trait loci were identified for almost all traits under investigation. The identified loci partially coincided with known mapped loci and partially identified new loci. Nine F3 populations were used to validate the QTLs and monitor the overall increase in the homozygosity level.