About

Dr. Marcelo Mollinari is an Assistant Research Professor in the College of Agriculture and Life Sciences at NC State University, located in Ricks Hall. His primary research interests lie in genetic statistics and its applications in understanding complex biological processes of polyploid species, which are species with more than two paired sets of chromosomes. His work focuses on developing and applying statistical and computational strategies to decode the inheritance patterns in these species, with a particular emphasis on plant breeding.

Research topics

• Computer Science
• Genetics
• Biology
• Machine Learning
• Artificial Intelligence
• Computational biology
• Agronomy
• Biotechnology
• Evolutionary biology
• Botany

Selected publications

• A single genomic region controls primocane fruiting in tetraploid blackberry

  Genetics · 2026-03-23

  articleOpen access

  The fresh-market blackberry (Rubus subgenus Rubus) industry has expanded dramatically in the past two decades, driven in part by improved cultivars. Introgression of the primocane-fruiting (PF; annual flowering) trait into elite germplasm has enabled dual cropping in a single year, season extension, and cultivation in tropical and subtropical regions. Despite its economic performance, the genetic basis of PF is not well understood. It has been proposed that the PF trait is controlled by a major recessive locus, but its genomic location is unclear. Here, a genome-wide association study (GWAS) of 365 tetraploid blackberry genotypes identified a single genomic region on chromosome Ra03 (∼33 Mb) strongly associated with PF. Genetic linkage analysis in a biparental population confirmed that the same interval (32-35 Mb) was linked to the PF phenotype. Ten putative candidate genes were identified in this region. Allele mining using whole-genome resequencing of 17 genotypes highlighted two high-priority candidates: a CCCH-type zinc finger gene and a ubiquitin-specific protease gene. Use of an improved Rubus argutus 'Hillquist' genome annotation (v1.2) enabled refined variant interpretation, including identification of regulatory 3' UTR polymorphisms in the zinc finger homolog. Two diagnostic KASP markers (PF1 and PF2), designed from the most significant GWAS SNPs, predicted the PF phenotype with over 96% accuracy in a validation panel of 494 tetraploid blackberries from multiple breeding programs. Together, these results provide the first high-resolution mapping of the PF locus in blackberry, identify candidate genes for flowering regulation in Rubus, and deliver diagnostic markers that can be immediately deployed in breeding programs.

  PublisherDOI

• Discovery of a major QTL for resistance to <i>Fusarium</i> wilt ( <i>Fusarium oxysporum</i> f. sp. <i>batatas</i> ) in the hexaploid Covington sweetpotato

  Crop Science · 2026-01-01

  articleOpen access

  Abstract Fusarium oxysporum f. sp. batatas , the causal agent of Fusarium wilt disease, was once the most damaging pathogen of sweetpotato in the United States. Breeding for cultivar resistance has largely addressed this issue, however, little is known about the genetic basis for resistance. Historically, sweetpotato breeders have relied on the high heritability of Fusarium wilt resistance, so identification of a region controlling resistance would be a major first step in implementing marker‐assisted selection for this trait. We assayed a biparental mapping population, NCDM04‐0001 × ‘Covington’ (DC), consisting of a susceptible by resistant cross composed of 454 progenies, for resistance to Fusarium wilt disease using visual assessments and an ordinal disease severity rating scale. Parental and check lines performed as expected, and the DC population exhibited segregation for resistance across trials over 3 years and in a joint analysis. We next performed quantitative trait locus (QTL) analyses using a linkage map based on the Ipomoea trifida diploid reference genome. Across multiple trials, we repeatedly detected a major QTL on chromosome 10, herein named qIbFo‐10.1. This QTL had a heritability of 33.8%, suggesting that a single locus explains a large amount of variation for resistance to this critically important trait. A basic local alignment search tool revealed several candidate genes: itf10g19820 (transcriptional factor B3 family protein/auxin‐responsive factor AUX/IAA‐related), four LRR‐kinases (leucine‐rich repeat receptor kinase) (itf10g21910, itf10g19200, itf10g19260, and itf10g20000), and two toll‐interleukin‐resistance genes (itf10g20200 and itf10g20220). Future efforts should develop molecular tools for Fusarium wilt resistance breeding, resulting in shorter breeding cycles and faster variety releases.

  PublisherOA PDFDOI

• Genetic linkage mapping in <i>Megathyrsus maximus</i> (Jacq.) with multiple dosage markers

  G3 Genes Genomes Genetics · 2025-07-16 · 1 citations

  articleOpen access

  Megathyrsus maximus (Jacq.), commonly known as guinea grass, is a forage crop widely used to form pastures and feed livestock. The species stands out for presenting high yield and nutritional quality in the leaves and its ability to be clonally propagated by seeds. In this work, we construct a dense and informative genetic linkage map for M. maximus using multiple dosage markers. We sequenced DNA from leaf samples of 224 individuals from a biparental cross between two tetraploid genotypes, then analyzed the raw sequencing data to find variants and call dosage-based genotypes using four related reference genomes. With the multiple dosage genotypes for both parents and all individuals, we constructed a highly informative genetic linkage map using state-of-the-art methods coupled with the multipoint Hidden Markov Model approach. We present the densest and most informative genetic linkage map to date for the species, with 7,095 markers distributed across eight homology groups, spanning 1573.31 cM of the genome. Both parents and all individuals in the mapping population were phased according to the species' ploidy level. There was no evidence of double-reduction or preferential pairing in the studied population. The linkage analysis provided in this work can help unravel the evolutionary pathway of the species, understand the genetic behavior of quantitative traits, assist in the assembly of reference genomes, and support the adoption of genomics-assisted selection strategies in M. maximus breeding programs.

  PublisherOA PDFDOI

• Linkage map construction and QTL mapping for morphological traits in <i>Ipomoea trifida</i> , a diploid sweetpotato relative

  The Plant Genome · 2025-09-01

  articleOpen access

  Ipomoea trifida G. Don (2n = 2x = 30) is considered the closest known diploid relative and a wild ancestor of the autohexaploid sweetpotato, Ipomoea batatas (L.) Lam. (2n = 6x = 90). This study aimed to map quantitative trait loci (QTLs) in a diploid full-sib population (M9 × M19) consisting of 210 progenies based on a high-density genetic linkage map constructed with single-nucleotide polymorphisms (SNPs). In a randomized complete block design with four replications, the phenotypic evaluation of 11 morphological traits was conducted for 188 individuals in 2016 at the International Potato Center under screenhouse conditions in San Ramón, Peru. Heritabilities ranged from 0.30 to 0.80, and genetic correlations varied from -0.22 to 1. An integrated genetic map was constructed with 15 linkage groups and 6410 SNPs spanning 2440.47 cM using the Onemap v.3.0 R package. Major misassemblies were identified and properly fixed on chromosomes 2, 3, and 7. QTL mapping was performed using the composite interval mapping approach for each trait with fullsibQTL v.0.0.901 R package. A total of 37 QTLs were identified, with up to 42.39% of the proportion of phenotypic variance explained by a major QTL on chromosome 3 for a leaf shape-related trait. Reference genome refining and QTL-linked markers contribute to advancing genetic and genomic research on I. trifida and may support sweetpotato breeding programs targeting ornamental traits.

  PublisherDOI

• A Single Genomic Region Controls Primocane Fruiting in Tetraploid Blackberry

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-17 · 1 citations

  articleOpen access

  Abstract The fresh-market blackberry ( Rubus subgenus Rubus ) industry has expanded dramatically in the past two decades, driven in part by improved cultivars. Introgression of the primocane-fruiting (PF; annual flowering) trait into elite germplasm has enabled dual cropping in a single year, season extension, and cultivation in tropical and subtropical regions. Despite its economic performance, the genetic basis of PF is not well understood. It has been proposed that the PF trait is controlled by a major recessive locus, but its genomic location is unclear. Here, a genome-wide association study (GWAS) of 365 tetraploid blackberry genotypes identified a single genomic region on chromosome Ra03 (∼33 Mb) strongly associated with PF. Genetic linkage analysis in a biparental population confirmed that the same interval (32-35 Mb) was linked to the PF phenotype. Ten putative candidate genes were identified in this region. Allele mining using whole-genome resequencing of 17 genotypes highlighted two high-priority candidates: a CCCH-type zinc finger gene and a ubiquitin-specific protease gene. Use of an improved Rubus argutus ‘Hillquist’ genome annotation (v1.2) enabled refined variant interpretation, including identification of regulatory 3′ UTR polymorphisms in the zinc finger homolog. Two diagnostic KASP markers ( PF1 and PF2 ), designed from the most significant GWAS SNPs, predicted the PF phenotype with over 96% accuracy in a validation panel of 494 tetraploid blackberries from multiple breeding programs. Together, these results provide the first high-resolution mapping of the PF locus in blackberry, identify candidate genes for flowering regulation in Rubus , and deliver diagnostic markers that can be immediately deployed in breeding programs.

  PublisherDOI

• Data from: Linkage map construction and QTL mapping for morphological traits in <em>Ipomoea trifida</em>, a diploid sweetpotato relative

  DRYAD · 2025-08-04

  datasetOpen access

  Sweetpotato (Ipomoea batatas) is an important food and ornamental polyploid crop with a complex genome. Its closest wild, diploid relative, Ipomoea trifida, emerges as a relatively simpler model for conducting genetic studies. Understanding the genetic basis of morphological traits in I. trifida can provide essential insights for improving agricultural and ornamental sweetpotato. We aimed to study the genetic architecture of morphological traits in an I. trifida full-sib family. Using a high-density genetic linkage map, we were able to unravel and fix major reference genome misassemblies in chromosomes 2, 3, and 7. In addition, 37 quantitative trait loci (QTL) for eleven morphological traits were identified, including major QTL for leaf morphological traits. These findings advance the genomic characterization of the Ipomoea genus, offering support for future efforts to improve agricultural and ornamental traits in a globally relevant crop such as sweetpotato.

  PublisherDOI

• Phased chromosome-level assembly provides insight into the genome architecture of hexaploid sweetpotato

  Nature Plants · 2025-08-08 · 10 citations

  article
  PublisherDOI

• Reliability and Usefulness of Seedling Plant Data in Cassava Breeding

  Plants · 2025-09-08

  articleOpen access

  Cassava breeding traditionally involves several years of phenotypic evaluation and field selection. The process begins with seedling evaluation trials (SETs), followed by single row trials (SRTs), and then progresses through preliminary, advanced and uniform yield trials. In recent years, significant efforts have been made to shorten the cassava breeding cycle through genomic selection, which relies on genotypically estimated breeding values (GEBVs). Breeders have typically performed visual selection during the SET stage, when each genotype in segregating populations is represented by a single plant. Despite the intense selection pressure applied at this stage-often eliminating 80-90% of genotypes-no data are collected prior to selection. As a result, breeders miss the opportunity to assess the degree and direction of dominance for key cassava traits, which remains largely unknown. This study provides pioneering insights based on seedling data collected over three years of field evaluations, along with the performance of selected genotypes at the SRT stage. Beyond its relevance for conventional inheritance studies, SET data can also be used to estimate phenotypically estimated breeding values (PEBVs) of progenitors, serving a similar purpose to GEBVs in genomic selection strategies. In fact, these two approaches to estimating breeding values can be highly complementary.

  PublisherOA PDFDOI

• Prediction of blueberry sensory texture attributes by integrating multiple instrumental measurements

  Postharvest Biology and Technology · 2024-08-28 · 10 citations

  article
  PublisherDOI

• A Public Mid-Density Genotyping Platform for Hexaploid Sweetpotato (Ipomoea batatas [L.] Lam)

  Genes · 2024-08-09 · 7 citations

  articleOpen access

  Small public breeding programs focused on specialty crops have many barriers to adopting technology, particularly creating and using genetic marker panels for genomic-based decisions in selection. Here, we report the creation of a DArTag panel of 3120 loci distributed across the sweetpotato (Ipomoea batatas [L.] Lam) genome for molecular-marker-assisted breeding and genomic prediction. The creation of this marker panel has the potential to bring cost-effective and rapid genotyping capabilities to sweetpotato breeding programs worldwide. The open access provided by this platform will allow the genetic datasets generated on the marker panel to be compared and joined across projects, institutions, and countries. This genotyping resource has the power to make routine genotyping a reality for any breeder of sweetpotato.

  PublisherOA PDFDOI

Frequent coauthors

• Antônio Augusto Franco Garcia

  Universidade de São Paulo

  40 shared

• Anete Pereira de Souza

  Universidade Estadual de Campinas (UNICAMP)

  28 shared

• Guilherme da Silva Pereira

  Agricultural Research Service

  26 shared

• Thiago G. Marconi

  North Carolina State University

  21 shared

• Luciana Rossini Pinto

  Agronomical Institute of Campinas

  20 shared

• K. M. Oliveira

  18 shared

• G. Craig Yencho

  North Carolina State University

  18 shared

• Zhao‐Bang Zeng

  18 shared

Education

• PhD, Genetics

  Universidade de São Paulo Escola Superior de Agricultura Luiz de Queiroz Departamento de Genética

  2012

• Master, Genetics

  Universidade de São Paulo Escola Superior de Agricultura Luiz de Queiroz Departamento de Genética

  2008

• Agronomist, Genetics

  Universidade de São Paulo Escola Superior de Agricultura Luiz de Queiroz

  2006