Biology subjects

Zeng, Z.-B.

Publications and source records attributed to Zeng, Z.-B..

8 recordsLinked to original sources

bioRxiv2025

A Theory of Heterosis

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 SummaryWe 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.

genetics↗

bioRxiv2024

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

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. SummaryThis 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.

genetics↗

bioRxiv2020

Quantitative trait locus mapping for common scab resistance in a tetraploid potato full-sib population

Despite the negative impact of common scab (Streptomyces spp.) to the potato industry, little is known about the genetic architecture of resistance to this bacterial disease in the crop. We evaluated a mapping population (~150 full-sibs) derived from a cross between two tetraploid potatoes ( Atlantic x B1829-5) in three environments (MN11, PA11, ME12) under natural common scab pressure. Three measures to common scab reaction were assessed, namely percentage of scabby tubers, and disease area and lesion indices, which were highly correlated (>0.76). Due to large environmental effect, heritability values were zero for all three traits in MN11, but moderate to high in PA11 and ME12 (0.44~0.79). We identified a single quantitative trait locus (QTL) for lesion index in PA11, ME12 and joint analyses on linkage group 3, explaining 22~30% of the total variation. The identification of QTL haplotypes and candidate genes contributing to disease resistance can support genomics-assisted breeding approaches.

genetics↗

bioRxiv2020

The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. 'Atlantic'-derived F1 population

There are many challenges involved with the genetic analyses of autopolyploid species, such as the tetraploid potato, Solanum tuberosum (2n = 4x = 48). The development of new analytical methods has made it valuable to re-analyze an F1 population (n = 156) derived from a cross involving Atlantic, a widely grown chipping variety in the USA. A fully integrated genetic map with 4,285 single nucleotide polymorphisms, spanning 1,630 cM, was constructed with MAPpoly software. We observed that bivalent configurations were the most abundant ones (51.0[~]72.4% depending on parent and linkage group), though multivalent configurations were also observed (2.2[~]39.2%). Seven traits were evaluated over four years (2006-8 and 2014) and quantitative trait loci (QTL) mapping was carried out using QTLpoly software. Based on a multiple-QTL model approach, we detected 21 QTL for 15 out of 27 trait-year combination phenotypes. A hotspot on linkage group 5 was identified as QTL for maturity, plant yield, specific gravity and internal heat necrosis resistance over different years were co-located. Additional QTL for specific gravity and dry matter were detected with maturity-corrected phenotypes. Among the genes around QTL peaks, we found those on chromosome 5 that have been previously implicated in maturity (StCDF1) and tuber formation (POTH1). These analyses have the potential to provide insights into the biology and breeding of tetraploid potato and other autopolyploid species.

genetics↗

bioRxiv2020

Sequencing depth and genotype quality: Accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops

The autopolyploid nature of potato and sweetpotato ensures a wide range of meiotic configurations and linkage phases leading to complex gene action and pose problems in genotype data quality and genomic selection analyses. We used a 315-progeny biparental population of hexaploid sweetpotato and a diversity panel of 380 tetraploid potato, genotyped using different platforms to answer the following questions: i) do polyploid crop breeders need to invest more for additional sequencing depth? ii) how many markers are required to make selection decisions? iii) does considering non-additive genetic effects improve predictive ability (PA)? iv) does considering dosage or quantitative trait loci (QTL) offer significant improvement to PA? Our results show that only a small number of highly informative single nucleotide polymorphisms (SNPs; [≤] 1000) are adequate for prediction, hence it is possible to get this number at the current sequencing depth from most service providers. We also show that considering dosage information and additive-effects only models had the best PA for most traits, while the comparative advantage of considering non-additive genetic effects and including known QTL in the predictive model depended on trait architecture. We conclude that genomic selection can help accelerate the rate of genetic gains in potato and sweetpotato. However, application of genomic selection should be considered as part of optimizing the entire breeding program. Additionally, since the predictions in the current study are based on single populations, further studies on the effects of haplotype structure and inheritance on PA should be studied in actual multi-generation breeding populations. Key messagePolypoid crop breeders do not need more investment for sequencing depth, dosage information and fewer highly informative SNPs recommended, non-additive models and QTL advantages on prediction dependent on trait architecture.

genetics↗

bioRxiv2019

Unraveling the hexaploid sweetpotato inheritance using ultra-dense multilocus mapping

The hexaploid sweetpotato (Ipomoea batatas (L.) Lam., 2n = 6x = 90) is an important staple food crop worldwide and has 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 implemented 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.

genetics↗

bioRxiv2019

Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population

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 only fit 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 bi-parental population ( Beauregard x Tanzania) with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly predicted 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 cM position. Multiple interval mapping was performed using our R package QTLPOLY and detected a total of 41 QTL, ranging from one to ten QTL per trait. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits and provided basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions allowed us to characterize additive allele effects as well as to compute 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.

genetics↗

bioRxiv2017

Assembly Of Whole-Chromosome Pseudomolecules For Polyploid Plant Genomes Using Outcrossed Mapping Populations

The assembly of whole-chromosome pseudomolecules for plant genomes remains challenging due to polyploidy and high repeat content. We developed an approach for constructing complete pseudomolecules for polyploid species using genotyping-by-sequencing data from outcrossing mapping populations coupled with high coverage whole genome sequence data of a reference genome. Our approach combines de novo assembly with linkage mapping to arrange scaffolds into pseudomolecules. We show that the method is able to reconstruct simulated chromosomes for both diploid and tetraploid genomes. Comparisons to three existing genetic mapping tools show that our method outperforms the other methods in accuracy on both grouping and ordering, and is robust to the presence of substantial amounts of missing data and genotyping errors. We applied our method to three real datasets including a diploid Ipomoea trifida and two tetraploid potato mapping populations. The linkage maps show significant concordance with the reference chromosomes. We resolved seven assembly errors for the published Ipomoea trifida genome assembly as well as anchored an unplaced scaffold in the published potato genome.

bioinformatics↗