The hexaploid sweetpotato (Ipomoea batatas (L.) Lam., 2n = 6x = 90) is an important staple food crop worldwide and plays a vital role in alleviating famine in developing countries. Due to its high ploidy level, genetic studies in sweetpotato lag behind major diploid crops significantly. We built an ultra-dense multilocus integrated genetic map and characterized the inheritance system in a sweetpotato full-sib family using our newly developed software, MAPpoly. The resulting genetic map revealed 96.5% collinearity between I. batatas and its diploid relative I. trifida. We computed the genotypic probabilities across the whole genome for all individuals in the mapping population and inferred their complete hexaploid haplotypes. We provide evidence that most of the meiotic configurations (73.3%) were resolved in bivalents, although a small portion of multivalent signatures (15.7%), among other inconclusive configurations (11.0%), were also observed. Except for low levels of preferential pairing in linkage group 2, we observed a hexasomic inheritance mechanism in all linkage groups. We propose that the hexasomic-bivalent inheritance promotes stability to the allelic transmission in sweetpotato.

In developing countries, the sweetpotato, Ipomoea batatas (L.) Lam. (2n=6x=90), is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can fit only a single QTL and are generally hard to interpret. Here, we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato biparental population (‘Beauregard’ × ‘Tanzania’) with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly adjusted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every centiMorgan position. Multiple interval mapping was performed using our R package QTLpoly and detected a total of 13 QTL, ranging from none to four QTL per trait, which explained up to 55% of the total variance. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits, and provided a basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions were decomposed into additive allele effects and were used to compute multiple QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids.

BackgroundSugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection. High-throughput next-generation sequencing (NGS) technologies have opened new opportunities for discovering molecular markers, especially single nucleotide polymorphisms (SNPs) and insertion-deletion (indels), at the genome-wide level. The objectives of this study were to (i) establish a pipeline for identifying variants from genotyping-by-sequencing (GBS) data in sugarcane, (ii) construct an integrated genetic map with GBS-based markers plus target region amplification polymorphisms and microsatellites, (iii) detect QTLs related to yield component traits, and (iv) perform annotation of the sequences that originated the associated markers with mapped QTLs to search putative candidate genes.ResultsWe used four pseudo-references to align the GBS reads. Depending on the reference, from 3,433 to 15,906 high-quality markers were discovered, and half of them segregated as single-dose markers (SDMs) on average. In addition to 7,049 non-redundant SDMs from GBS, 629 gel-based markers were used in a subsequent linkage analysis. Of 7,678 SDMs, 993 were mapped. These markers were distributed throughout 223 linkage groups, which were clustered in 18 homo(eo)logous groups (HGs), with a cumulative map length of 3,682.04 cM and an average marker density of 3.70 cM. We performed QTL mapping of four traits and found seven QTLs. Our results suggest the presence of a stable QTL across locations. Furthermore, QTLs to soluble solid content (BRIX) and fiber content (FIB) traits had markers linked to putative candidate genes.ConclusionsThis study is the first to report the use of GBS for large-scale variant discovery and genotyping of a mapping population in sugarcane, providing several insights regarding the use of NGS data in a polyploid, non-model species. The use of GBS generated a large number of markers and still enabled ploidy and allelic dosage estimation. Moreover, we were able to identify seven QTLs, two of which had great potential for validation and future use for molecular breeding in sugarcane.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3383-x) contains supplementary material, which is available to authorized users.

Key message β-Carotene content in sweetpotato is associated with the Orange and phytoene synthase genes; due to physical linkage of phytoene synthase with sucrose synthase, β-carotene and starch content are negatively correlated. Abstract In populations depending on sweetpotato for food security, starch is an important source of calories, while β-carotene is an important source of provitamin A. The negative association between the two traits contributes to the low nutritional quality of sweetpotato consumed, especially in sub-Saharan Africa. Using a biparental mapping population of 315 F 1 progeny generated from a cross between an orange-fleshed and a non-orange-fleshed sweetpotato variety, we identified two major quantitative trait loci (QTL) on linkage group (LG) three (LG3) and twelve (LG12) affecting starch, β-carotene, and their correlated traits, dry matter and flesh color. Analysis of parental haplotypes indicated that these two regions acted pleiotropically to reduce starch content and increase β-carotene in genotypes carrying the orange-fleshed parental haplotype at the LG3 locus. Phytoene synthase and sucrose synthase, the rate-limiting and linked genes located within the QTL on LG3 involved in the carotenoid and starch biosynthesis, respectively, were differentially expressed in Beauregard versus Tanzania storage roots. The Orange gene, the molecular switch for chromoplast biogenesis, located within the QTL on LG12 while not differentially expressed was expressed in developing roots of the parental genotypes. We conclude that these two QTL regions act together in a cis and trans manner to inhibit starch biosynthesis in amyloplasts and enhance chromoplast biogenesis, carotenoid biosynthesis, and accumulation in orange-fleshed sweetpotato. Understanding the genetic basis of this negative association between starch and β-carotene will inform future sweetpotato breeding strategies targeting sweetpotato for food and nutritional security.

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