Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte

Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to large-effect mutations versus variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load in the maize population that we predicted from sequence data. Parental breeding values were highly consistent between outcross and selfed offspring, indicating that additive effects determine most of the genetic value even in the presence of strong inbreeding depression. We developed a novel linkage scan to identify quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, smalleffect partially recessive effects in linkage disequilibrium underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against some large effect variants, but polygenic load is harder to purge and overall segregating mutational burden increased in maize compared to teosinte

Interrelations of α- and β-amylase activity with starch, sugars, and culinary and nutritional quality attributes in sweetpotato storage roots

BACKGROUND Little information is available on α- and β-amylase activity and their associations with starch, sugars and other culinary qualities in sweetpotato. The objective of this study was to assess sweetpotato storage root α- and β-amylase activity in relation to starch, sugars, β-carotene content and storage root flesh color. RESULTS α- and β-amylase activity (α-AA and β-AA) were assayed from a Tanzania (T) x Beauregard (B) genetic mapping population in their uncured (raw), cured and stored (~ 11 weeks) forms during 2016 and 2017. The Ceralpha and Betamyl methods, with modifications to suit a high-throughput microplate assay format, were used to quantify α-AA and β-AA, respectively. Storage root dry matter, starch, glucose, fructose, sucrose, and β-carotene content were predicted using near infrared reflectance spectroscopy (NIRS). There was little relationship (r2 = 0.02–0.08, p-value ≤0.05 in 2016 and r2 = 0.05–0.11, p-value ≤0.05 in 2017) between α-AA and β-AA. We observed negative linear associations between α-AA and dry matter content and generally no correlations between β-AA and dry matter content. β-AA and sugars were weakly positively correlated. β-AA and β-carotene content were positively correlated (r = 0.3–0.4 in 2016 and 0.3–0.5 in 2017). CONCLUSIONS Generally, the correlation coefficient for amylase enzyme activity and sugar components of storage roots at harvest increased after curing and during post-harvest storage. This study is a major step forward in sweetpotato breeding by providing a better understanding of how α- and β-amylase activity are inter-associated with several culinary quality attributes

Discovery of a major QTL for root-knot nematode (Meloidogyne incognita) resistance in cultivated sweetpotato (Ipomoea batatas)

The root-knot nematode [Meloidogyne incognita (Kofoid & White) Chitwood] (RKN) causes significant storage root quality reduction and yields losses in cultivated sweetpotato [Ipomoea batatas (L.) Lam.]. In this study, resistance to RKN was examined in a mapping population consisting of 244 progenies derived from a cross (TB) between ‘Tanzania,’ a predominant African landrace cultivar with resistance to RKN, and ‘Beauregard,’ an RKN susceptible major cultivar in the USA. We performed quantitative trait loci (QTL) analysis using a random-effect QTL mapping model on the TB genetic map. An RKN bioassay incorporating potted cuttings of each genotype was conducted in the greenhouse and replicated five times over a period of 10 weeks. For each replication, each genotype was inoculated with ca. 20,000 RKN eggs, and root-knot galls were counted ~62 days after inoculation. Resistance to RKN in the progeny was highly skewed toward the resistant parent, exhibiting medium to high levels of resistance. We identified one major QTL on linkage group 7, dominant in nature, which explained 58.3% of the phenotypic variation in RKN counts. This work represents a significant step forward in our understanding of the genetic architecture of RKN resistance and sets the stage for future utilization of genomics-assisted breeding in sweetpotato breeding programs

Genotype by Environment (G x E) Modeling of the Variable Initiation of Parthenocarpy sensu stricto in Musa: Elucidation of the Environmental Components of Variable Expressivity of Parthenocarpy in a Facultative Apomictic Musa acuminata Subspecies Microcarpa Model System

To better understand the genome by environment (G x E) interactions that need to be accommodated in order to better predict hybrid performance for a high breeding value vegetative parthenocarpy trait sensu stricto. An analysis of the possible environmental signals contributing to the variability of a vegetative parthenocarpy trait sensu stricto via the genome x environment initiation of a genetic lesion that temporally, developmentally and systematically results in abortion of a parthenocarpic developmental regime was performed utilizing Musa acuminata accession Borneo as a model plant. We examined the effect of the variable and potentially modulating environmental signals, and performed a dissection of the genetic components of expressivity and penetrance in the vegetative parthenocarpy in Borneo, utilizing 180 apomictic progeny planted at different developmental ages in duplicate at each of two ecoregional zones. A total of 2,160 floral rachis from 720 mats of Borneo were measured for their subsequent expressivity and penetrance for vegetative parthenocarpy across individual flowers produced from a single vegetative mat, across local duplicate mats, and across ecoregional zones. The results of our study have produced a predictive G x E Model for expressivity of vegetative parthenocarpy in Musa, with validation of this model by a variety of statistical and probabilistic methods. Since expressivity of vegetative parthenocarpy to similar environmental signals have been identified across the monocot to dicot plants such as tomato, the generalized use of models such as presented in our study may have broader applicability to a wider range of crop plants

Development of NIRS Calibration Curves for Sugars in Baked Sweetpotato

Background Variability in sugar content between raw and cooked sweetpotato storage roots impact nutritional and dietary importance with implications for consumer preference. High-throughput phenotyping is required to breed varieties that satisfy consumer preferences. Results Near-infrared reflectance spectroscopy (NIRS) calibration curves were developed for analyzing sugars in baked storage roots using 147 genotypes from a population segregating for sugar content and other traits. The NIRS prediction curves had high coefficients of determination in calibration (R2c) of 0.96 (glucose), 0.93 (fructose), 0.96 (sucrose), and 0.96 (maltose). The corresponding coefficients of determination for cross validation (R2cv) were 0.92 (glucose), 0.89 (fructose), 0.96 (sucrose) and 0.93 (maltose) and were similar to the R2c for all sugars measured. The ratios of the standard deviation of the reference set to the standard error of cross validation were greater than three for all sugars. These results confirm the applicability of the NIRS curves in efficiently determining sugar content in baked sweetpotatoes storage roots. External validation was performed on an additional 70 genotypes. Coefficients of determination (r2) were 0.88 (glucose), 0.88 (fructose), 0.86 (sucrose) and 0.49 (maltose). The results were comparable to those found for the calibration and cross validation in fructose, glucose, and sucrose, but were moderate for maltose due to the low variability of maltose content in the population. Conclusions NIRS can be used for screening sugar content in baked sweetpotato storage roots in breeding programs and can be used to assist with the development of improved sweetpotato varieties that better meet consumer preferences

The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication.

The genetics of domestication has been extensively studied ever since the rediscovery of Mendel's law of inheritance and much has been learned about the genetic control of trait differences between crops and their ancestors. Here, we ask how domestication has altered genetic architecture by comparing the genetic architecture of 18 domestication traits in maize and its ancestor teosinte using matched populations. We observed a strongly reduced number of QTL for domestication traits in maize relative to teosinte, which is consistent with the previously reported depletion of additive variance by selection during domestication. We also observed more dominance in maize than teosinte, likely a consequence of selective removal of additive variants. We observed that large effect QTL have low minor allele frequency (MAF) in both maize and teosinte. Regions of the genome that are strongly differentiated between teosinte and maize (high FST) explain less quantitative variation in maize than teosinte, suggesting that, in these regions, allelic variants were brought to (or near) fixation during domestication. We also observed that genomic regions of high recombination explain a disproportionately large proportion of heritable variance both before and after domestication. Finally, we observed that about 75% of the additive variance in both teosinte and maize is "missing" in the sense that it cannot be ascribed to detectable QTL and only 25% of variance maps to specific QTL. This latter result suggests that morphological evolution during domestication is largely attributable to very large numbers of QTL of very small effect

The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication.

The genetics of domestication has been extensively studied ever since the rediscovery of Mendel's law of inheritance and much has been learned about the genetic control of trait differences between crops and their ancestors. Here, we ask how domestication has altered genetic architecture by comparing the genetic architecture of 18 domestication traits in maize and its ancestor teosinte using matched populations. We observed a strongly reduced number of QTL for domestication traits in maize relative to teosinte, which is consistent with the previously reported depletion of additive variance by selection during domestication. We also observed more dominance in maize than teosinte, likely a consequence of selective removal of additive variants. We observed that large effect QTL have low minor allele frequency (MAF) in both maize and teosinte. Regions of the genome that are strongly differentiated between teosinte and maize (high FST) explain less quantitative variation in maize than teosinte, suggesting that, in these regions, allelic variants were brought to (or near) fixation during domestication. We also observed that genomic regions of high recombination explain a disproportionately large proportion of heritable variance both before and after domestication. Finally, we observed that about 75% of the additive variance in both teosinte and maize is "missing" in the sense that it cannot be ascribed to detectable QTL and only 25% of variance maps to specific QTL. This latter result suggests that morphological evolution during domestication is largely attributable to very large numbers of QTL of very small effect

The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication.

The genetics of domestication has been extensively studied ever since the rediscovery of Mendel's law of inheritance and much has been learned about the genetic control of trait differences between crops and their ancestors. Here, we ask how domestication has altered genetic architecture by comparing the genetic architecture of 18 domestication traits in maize and its ancestor teosinte using matched populations. We observed a strongly reduced number of QTL for domestication traits in maize relative to teosinte, which is consistent with the previously reported depletion of additive variance by selection during domestication. We also observed more dominance in maize than teosinte, likely a consequence of selective removal of additive variants. We observed that large effect QTL have low minor allele frequency (MAF) in both maize and teosinte. Regions of the genome that are strongly differentiated between teosinte and maize (high FST) explain less quantitative variation in maize than teosinte, suggesting that, in these regions, allelic variants were brought to (or near) fixation during domestication. We also observed that genomic regions of high recombination explain a disproportionately large proportion of heritable variance both before and after domestication. Finally, we observed that about 75% of the additive variance in both teosinte and maize is "missing" in the sense that it cannot be ascribed to detectable QTL and only 25% of variance maps to specific QTL. This latter result suggests that morphological evolution during domestication is largely attributable to very large numbers of QTL of very small effect