Linkage Mapping and QTL Analysis

Training presentations


  • MAPpoly, QTLpoly, and VIEWpoly updates: Use, progress and case studies - presented by Marcelo Mollinari, Gabriel Gesteira and Cris Taniguti. In this workshop, we will show how to construct genetic maps and perform QTL analysis in multiparental polyploid populations using new versions of the R packages MAPpoly and QTLpoly. In the hands-on section, we will use a tetraploid dataset to show the software features and present results in three interconnected hexaploid sweetpotato populations. We will also introduce VIEWpoly, an R package for visualizing and exploring results from polyploid computational tools using an interactive graphical user interface.
  • Polyploid Linkage and QTL Mapping with polymapR and polyqtlR - presented by Peter Bourke et al. In this workshop, participants will be re-acquainted with Wageningen’s polymapR / polyqtlR pipeline for linkage map construction and QTL analysis in polyploid F1 populations. Demonstration of new or extra software features not previously covered will be highlighted. These include using probabilistic genotypes in place of discrete genotypes, automatic building of multi-QTL models via co-factor analysis, visualizing meiotic pairing behavior, and genotype curation (spotting and correcting genotyping errors).



User presentations

Jibran Tahir and Cyril Brendolise. The New Zealand Institute of Plant and Food Research. 

            Polyploidy is a key driver of significant evolutionary changes in plant species. The genus Actinidia (kiwifruit) exhibits multiple ploidy levels, which contribute to novel fruit traits, high yields, and resistance to the pathogen. Breeding programs focus on tetraploid cultivars, because of their resilience to the Psa disease, as well as robust fruit quality traits and size. However, there remains a substantial knowledge gap concerning the chromosomal biology and complex gene-trait associations in polyploid kiwifruit, which also exhibits high heterozygosity due to dioecy, compared with diploid species. Here we present the first case study where we employed CaptureSeq for genotyping 235 F1 heterozygous individuals of a tetraploid kiwifruit mapping population using 10K baits which generated a total of 725,175 raw SNP variants. Using this dataset we first identified caveats in the population structure by studying kinship and recombination landscape. We then performed dosage counts, using an empirical Bayesian analysis (Updog, “normal model”), and selected 45,436 high-quality SNPs across 188 F1s for generating ultra-dense linkage maps for 29 chromosomes, using polymapR. To further assess the quality of our maps, we estimated the Identity-by-descent (IBD) probabilities. We also tested the nature of pairing among chromosomes and provided the first evidence from a mapping population that the inheritance in polyploid kiwifruit species is mostly polysomic with preferential pairing in a few LGs. Finally, we performed QTL mapping for two key polygenic traits for breeding (bacterial resistance and flowering) and a monogenic trait for breeding operation (sex) and calculated the additive effects from various QTLs for a trait. We also tested an HRM-based SNP marker workflow downstream of QTL mapping, to assess the possibility of marker-assisted selection for these traits. Our study provides a detailed view of multiple challenges and successes in solving the genetic maze of polygenic traits in a polyploid dioecious species.


Paterne Agre, Kumar Lava, Robert Asiedu, Asrat Asfaw. International Institute of Tropical Agriculture, Ibadan, Nigeria.

            Anthracnose disease, caused by the fungus Colletotrichum gloeosporioides, is the primary cause of yield loss in water yam (Dioscorea alata), the widely cultivated species of yam. Resistance to yam anthracnose disease (YAD) is a prime target in breeding initiatives to develop cultivars with durable resistance for the sustainable management of the disease in water yam cultivation. This study aimed at tagging quantitative trait loci (QTL) for anthracnose disease resistance in a bi-parental mapping population of D. alata. Parent genotypes and their recombinant progenies were genotyped using the GBS platform and phenotyped in two crop cycles for two years. A high-density genetic linkage map was built with 3,184 polymorphic SNP markers well distributed across the genome covering 1460.94 cm total length. On average 163 SNP markers were mapped per chromosome with 0.58 genetic distance between SNPs. Four QTL regions related to yam anthracnose disease resistance were identified on 3 chromosomes. The proportion of phenotypic variance explained by these QTLs ranged from 29.54 to 39.40%. The QTL regions identified showed genes that code for known plant defense responses such as GDSL-like Lipase/Acylhydrolase, Protein kinase domain, and F-box protein. The results from the present study provide valuable insight into the genetic architecture of anthracnose resistance in water yam. The candidate markers identified herewith form a relevant resource to apply marker-assisted selection as an alternative to a conventional labor-intensive screening for anthracnose resistance in water yam.

Poster presentations

Simon Fraher1, Tanner Schwarz2, Bonny Oloka3, Ken Pecota1, Chris Heim1, Adrienne Gorny2, G. Craig Yencho1. 1Department of Horticultural Science, North Carolina State University, Raleigh, NC. 2Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC. 3Root Crops Program, National Agricultural Research Organization, Entebbe, Uganda.

Due to its highly heterozygous hexaploid nature, sweetpotato (I. batatas) lags behind other crops in terms of genomic tools. New tools and strategies have afforded opportunities to associate sequence data with phenotypic data through QTL analysis, especially the publication of a diploid reference genome for I. trifida in 2018, and open-source software packages like QTLpoly and MAPpoly. QTL analysis is expected to be instrumental in accelerating breeding in this crop, notably for nematode resistance and nutritional factors. We analyzed the progeny of the sweetpotato biparental mapping population ‘Tanzania’ x ‘Beauregard’ (TB) representing 250 genotypes (including 4 check lines) for resistance to the emergent plant-parasitic nematode, Meloidogyne enterolobii (M.e.). Parent ‘Tanzania’ is highly resistant, and parent ‘Beauregard’ is highly susceptible. Bioassays showed clear bimodal segregation for resistance, suggesting a simplex major allele conferring resistance. Using the R package QTLpoly and the I. trifida reference genome, we discovered a major QTL peak at base pair 7,039,636 (79.21cM) of linkage group 4 of I. batatas associated with resistance to M.e. This analysis suggests variability in M.e. resistance within the TB population can largely be ascribed to genetic differences amongst the progenies (h² =66.9%). The next steps will search for flanking markers associated with these genotypes and attempt to identify markers that can be screened in the seedling stage, reducing the need for costly and laborious bioassays with this quarantined pest.


Jose Guillermo Chacon1, Marcelo Mollinari1, Bode A. Olukolu2, Zhao-Bang Zeng1, Gina E. Fernandez3. 1Department of Horticultural Science, North Carolina State University, Raleigh, NC. 2Department of Entomology and Plant Physiology, University of Tennessee, Knoxville, TN. 3Bioinformatics Research Center, North Carolina State University, Raleigh, NC. 

                The cultivated strawberry (Fragaria ×ananassa L.) is an allopolyploid (2n= 8x = 28) with a complex genomic composition that hindered genetic and genomic studies, as the similarity between subgenomes, introgressions from a dominant genome, and other issues complicate accurate mapping and variant calling. The recent publication of a full chromosome length reference genome and improvements of deep sequencing for polyploids facilitated overcoming part of those difficulties, including the development of linkage maps. A biparental population was generated crossing the NCSU selections NCS 10-080 × NCS 10-147. The parents and 280 seedlings were sequenced using the reduced representation sequencing OmeSeq protocol resulting in 2.47 billion reads. The ngsComposer application was used for quality control, demultiplexing, and filtering, resulting in 1.84 billion reads. The read alignment resulted in a coverage of 92.32% of the four subgenomes in the allo-octoploid strawberry reference genome ‘Camarosa’ 1.0. The map construction was done using the MAPpoly R package. After a quality control screening, a total of 6133 markers and 212 offspring individuals were used to build a genetic linkage map comprised of 28 linkage groups with a total length of 3154 cM and 4022 SNP makers. The minimum linkage group size was 30.2 cM and 49 markers, and a maximum of 155.69 cM and 168 markers, with an average interval genetic distance of 1.32 cm. The high marker density and the correspondence between the number of assembled linkage groups and the number of expected chromosomes indicates that MAPpoly R is a robust analysis. This analysis provides an excellent framework map for forthcoming studies, including QTL analysis and understanding modes of inheritance in this complex polyploid species.


Haramrit Gill, Jeekin Lau, Qiuyi Fu, Natalie Anderson, David H. Byrne, and Oscar Riera-Lizarazu. Texas A&M University, College Station, TX.

                Flower color is one of the most important breeding traits in ornamental roses. The combination of particular anthocyanins, their co-factors, and their concentrations leads to different pigmentation patterns. We observed an interesting characteristic that we call ‘flower color transition’ in two tetraploid rose populations a) ‘Stormy Weather’ (SW) X ‘Brite Eyes’ (BE), b) ‘My Girl’ (MG) X ‘Brite Eyes’ (BE). The roses that exhibit this phenotype have flowers that transition from a light-yellow color to a dark pink/red (accumulation of anthocyanins) as the flower ages leading to bushes peppered with flowers of multiple colors. To our knowledge, the genetic control of this phenotype has not been studied in roses previously. Here, we present studies to better understand the inheritance of this trait and to identify quantitative trait loci (QTL) in two tetraploid bi-parental populations segregating for the ‘flower color transition’ trait. Our analysis suggests the presence of QTL on chromosomes 3 and 4. The location of QTL identified for the flower color transition coincides with the location of some genes involved in the flavonoid biosynthetic pathway. Additional studies are underway to validate these results.