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

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.

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

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

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.

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

The Plant Genome · 2025-09-01

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.

A Theory of Heterosis

bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-27

Abstract Heterosis refers to the superior performance of a hybrid over its parents. It is the basis for hybrid breeding particularly for maize and rice. Genetically it is due to interactions between alleles of quantitative trait loci (QTL) (dominance and epistasis). Despite enormous interest and efforts to study the genetic basis of heterosis, the relative contribution of dominance vs. epistasis to heterosis is still not clear. This is because most published studies estimate QTL effects in pieces, not able to put them together to assess the overall pattern adequately. We propose a theoretical framework that focuses on the inference of the relationship between genome and traits that includes the identification of multiple QTL and estimation of the whole set of QTL (additive, dominant, and epistatic) effects. Used for heterosis, it gives a clear genetic definition and interpretation of heterosis. We applied the theory and methods to a large maize dataset with a factorial design of many male and female inbred lines and their hybrid crosses. Heterosis of ear weight in maize is primarily due to QTL dominant effects, many are over-dominant. The contribution to heterosis due to epistasis is small and diffused. For comparison, we also analyzed a rice dataset that is an F2-type population derived from a cross between two inbred lines. The result indicates that dominance is still the main contributor to heterosis, and epistasis contribution is small. Article Summary We propose a general theoretical framework to analyze and interpret quantitative trait genetic variation in a population through the identification of quantitative trait loci (QTL) and the estimation of QTL effects including interactions. Applied to a large genomic study in maize, we produce direct estimation of genetic contribution to heterosis—QTL dominance and epistasis and compare them to the observed heterosis. The evidence is clear that the heterosis of ear weight in maize is primarily due to QTL dominance. The contribution to heterosis due to QTL epistasis is relatively small and diffused.

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

DRYAD · 2025-08-04

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.

A theory of heterosis

Genetics · 2025-03-18 · 2 citations

Heterosis refers to the superior performance of a hybrid over its parents. It is the basis for hybrid breeding particularly for maize and rice. Genetically, it is due to interactions between alleles of quantitative trait loci (dominance and epistasis). Despite enormous interest and efforts to study the genetic basis of heterosis, the relative contribution of dominance vs epistasis to heterosis is still not clear. This is because most published studies estimate quantitative trait loci effects in pieces, not able to put them together to assess the overall pattern adequately. We propose a theoretical framework that focuses on the inference of the relationship between genome and traits that includes the identification of multiple quantitative trait loci and estimation of the whole set of quantitative trait loci (additive, dominant, and epistatic) effects. Used for heterosis, it gives a clear genetic definition and interpretation of heterosis. We applied the theory and methods to a large maize dataset with a factorial design of many male and female inbred lines and their hybrid crosses. Heterosis of ear weight in maize is primarily due to quantitative trait loci dominant effects, many are overdominant. The contribution to heterosis due to epistasis is small and diffused. For comparison, we also analyzed a rice dataset that is an F2-type population derived from a cross between 2 inbred lines. The result indicates that dominance is still the main contributor to heterosis, and epistasis contribution is small.

Gut length evolved under sexual conflict in Lake Malawi cichlids

Genetics · 2025-05-26 · 1 citations

Variation in gastrointestinal morphology is associated with dietary specialization across the animal kingdom. Gut length generally correlates with trophic level, and increased gut length in herbivores is a classic example of adaptation to cope with diets having a lower nutrient content and a higher proportion of refractory material. However, the genetic basis of gut length variation remains largely unstudied, partly due to the inaccessibility and plasticity of the gut tissue, as well as the lack of dietary diversity within traditional model organisms relative to that observed among species belonging to different trophic levels. Here, we confirm the genetic basis of gut length variation among recently evolved Lake Malawi cichlid fish species with different dietary adaptations. We then produce interspecific, intertrophic-level hybrids to map evolved differences in intestinal length in an F2 mapping cross between Metriaclima mbenjii, an omnivore with a relatively long gut, and Aulonocara koningsi, a carnivore with a relatively short gut. We identify numerous candidate quantitative trait loci for evolved differences in intestinal length. These quantitative trait loci are predominantly sex-specific, supporting an evolutionary history of sexual conflicts for the gut. We also identify epistatic interactions potentially associated with canalization and the maintenance of cryptic variation in the cichlid adaptive radiation. Overall, our results suggest a complex, polygenic evolution of gut length variation associated with trophic level differences among cichlids, as well as conflicts and interactions that may be involved in evolutionary processes underlying other traits in cichlids.

Trophic level associated gut length divergence evolved under sexual conflict in Lake Malawi cichlids

bioRxiv (Cold Spring Harbor Laboratory) · 2024-12-11

Abstract Variation in gastrointestinal morphology is associated with dietary specialization across the animal kingdom. Gut length generally correlates with trophic level, and increased gut length in herbivores is a classic example of adaptation to cope with diets with lower nutrient content and a higher proportion of refractory material. However, the genetic basis of gut length variation remains largely unstudied, partly due to the inaccessibility and plasticity of the gut tissue, as well as the lack of dietary diversity within traditional model organisms relative to that observed among species belonging to different trophic levels. Here, we confirm the genetic basis of gut length variation among recently evolved Lake Malawi cichlid fish species with different dietary adaptations. We then produce interspecific, inter-trophic-level hybrids to map evolved differences in intestinal length in an F2 mapping cross between Metriaclima mbenjii , an omnivore with a relatively long gut, and Aulonocara koningsi , a carnivore with a relatively short gut. We identify numerous candidate quantitative trait loci for evolved differences in intestinal length. These quantitative trait loci are predominantly sex-specific, supporting an evolutionary history of sexual conflicts for the gut. We also identify epistatic interactions potentially associated with canalization and the maintenance of cryptic variation in the cichlid adaptive radiation. Overall, our results suggest a complex, polygenic evolution of gut length variation associated with trophic level differences among cichlids, as well as conflicts and interactions that may be involved in evolutionary processes underlying other traits in cichlids. Summary This study examines the genetic basis of gut length variation in Lake Malawi cichlids, which exhibit different dietary adaptations. It highlights how cichlids recapitulate a broad taxonomic trend: gut length correlates with trophic level, with herbivores and omnivores having longer intestines than carnivores. By creating hybrids of Metriaclima mbenjii (omnivore) and Aulonocara koningsi (carnivore), we identify several quantitative trait loci and epistatic interactions underlying gut length differences. These genetic associations are predominantly sex-specific, suggesting historical sexual conflicts. The results indicate complex, polygenic evolution of gut morphology in these fish, and suggest evolutionary interactions and processes shaping dietary traits across species.

New Analytical Tools for Molecular Mapping of Quantitative Trait Loci in Sweetpotato

Compendium of plant genomes · 2024-09-21

Abstract Quantitative trait loci(QTL) mapping is an important tool in sweetpotato research, contributing to the understanding of genetic architecture of various traits, including dry matter, nematode resistance, and flesh color. Early QTL work was carried out by using marker information alone via single marker analysis (SMA), or based on parent-specific linkage map using interval mapping (IM), composite interval mapping (CIM), and multiple interval mapping (MIM). Initially developed for inbred diploid species populations, these methods did not fully consider the complex autopolyploid, outcrossing nature of sweetpotato. Technological and methodological advances made it possible to obtain integrated, fully phased genetic maps for the crop. A random-effect MIM approach that leverages identity-by-descent based on QTL genotype conditional probabilities has been employed since with increasing power and resolution. To illustrate QTL identification in sweetpotato, we used publicly available data from ‘Beauregard’ × ‘Tanzania’ full-sib family ( $$N = 315$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>N</mml:mi> <mml:mo>=</mml:mo> <mml:mn>315</mml:mn> </mml:mrow> </mml:math> ) evaluated for flesh color in Peru. Several methods were able to detect two QTL on chromosomes 3 and 12 each for this trait in the same genomic regions. Despite the importance of such methods, there is need to extend existing models to account for multi-trait or multi-environment data and to evaluate their application in genomic-enabled prediction.

Discovery of a major QTL for resistance to the guava root-knot nematode (Meloidogyne enterolobii) in ‘Tanzania’, an African landrace sweetpotato (Ipomoea batatas)

Research Square · 2024-07-24