Insights into the Effects of Long-Term Artificial Selection on Seed Size in Maize

Grain produced from cereal crops is a primary source of human food and animal feed worldwide. To understand the genetic basis of seed-size variation, a grain yield component, we conducted a genome-wide scan to detect evidence of selection in the maize Krug Yellow Dent long-term divergent seed-size selection experiment. Previous studies have documented significant phenotypic divergence between the populations. Allele frequency estimates for ∼3 million single nucleotide polymorphisms (SNPs) in the base population and selected populations were estimated from pooled whole-genome resequencing of 48 individuals per population. Using F_ST values across sliding windows, 94 divergent regions with a median of six genes per region were identified. Additionally, 2729 SNPs that reached fixation in both selected populations with opposing fixed alleles were identified, many of which clustered in two regions of the genome. Copy-number variation was highly prevalent between the selected populations, with 532 total regions identified on the basis of read-depth variation and comparative genome hybridization. Regions important for seed weight in natural variation were identified in the maize nested association mapping population. However, the number of regions that overlapped with the long-term selection experiment did not exceed that expected by chance, possibly indicating unique sources of variation between the two populations. The results of this study provide insights into the genetic elements underlying seed-size variation in maize and could also have applications for other cereal crops.     

The Effects of Demography and Long-Term Selection on the Accuracy of Genomic Prediction with Sequence Data

The use of dense SNPs to predict the genetic value of an individual for a complex trait is often referred to as “genomic selection” in livestock and crops, but is also relevant to human genetics to predict, for example, complex genetic disease risk. The accuracy of prediction depends on the strength of linkage disequilibrium (LD) between SNPs and causal mutations. If sequence data were used instead of dense SNPs, accuracy should increase because causal mutations are present, but demographic history and long-term negative selection also influence accuracy. We therefore evaluated genomic prediction, using simulated sequence in two contrasting populations: one reducing from an ancestrally large effective population size (N_e) to a small one, with high LD common in domestic livestock, while the second had a large constant-sized N_e with low LD similar to that in some human or outbred plant populations. There were two scenarios in each population; causal variants were either neutral or under long-term negative selection. For large N_e, sequence data led to a 22% increase in accuracy relative to ∼600K SNP chip data with a Bayesian analysis and a more modest advantage with a BLUP analysis. This advantage increased when causal variants were influenced by negative selection, and accuracy persisted when 10 generations separated reference and validation populations. However, in the reducing N_e population, there was little advantage for sequence even with negative selection. This study demonstrates the joint influence of demography and selection on accuracy of prediction and improves our understanding of how best to exploit sequence for genomic prediction.     

Mapping QTL for Grain Yield and Plant Traits in a Tropical Maize Population

The vast majority of reported QTL mapping for maize (Zea mays L.) traits are from temperate germplasm and, also, QTL by environment interaction (QTL × E) has not been thoroughly evaluated and analyzed in most of these papers. The maize growing areas in tropical regions are more prone to environmental variability than in temperate areas, and, therefore, genotype by environment interaction is of great concern for maize breeders. The objectives of this study were to map QTL and to test their interaction with environments for several traits in a tropical maize population. Two-hundred and fifty-six F_2:3 families evaluated in five environments, a genetic map with 139 microsatellites markers, and the multiple-environment joint analysis (mCIM) were used to map QTL and to test QTL × E interaction. Sixteen, eight, six, six, nine, and two QTL were mapped for grain yield, ears per plant, plant lodging, plant height, ear height, and number of leaves, respectively. Most of these QTL interacted significantly with environments, most of them displayed overdominance for all traits, and genetic correlated traits had a low number of QTL mapped in the same genomic regions. Few of the QTL mapped had already been reported in both temperate and tropical germplasm. The low number of stable QTL across environments imposes additional challenges to design marker-assisted selection in tropical areas, unless the breeding programs could be directed towards specific target areas.     

海拔对全缘叶绿绒蒿植株性状和花特征的表型选择分析

为了研究海拔差异对植株性状、花特征表型选择的影响,以青藏高原高寒草甸的全缘叶绿绒蒿（Meconopsis integrifolia）为研究材料,于盛花期内,测定不同海拔（4 452、4 081和3 681 m）种群中个体植株性状、花特征、单果结实数并进行统计分析,采用线性回归模型估计不同海拔种群间植株性状、花特征所受的表型选择（选择差与选择梯度）。结果表明：（1）随着海拔升高,全缘叶绿绒蒿植株性状、花特征及单果结实数显著降低,海拔越高的种群中株高越矮、叶面积越小、花数越少、花越小、单果结实数越低。（2）不同海拔种群中各性状的表型选择存在差异,较低海拔（3 681 m）种群中花数、花大小具有显著的选择差和选择梯度,表现为花越多、花越大的个体雌性适合度越高;海拔较高（4 081 m）的种群中株高、叶面积及花数更容易受到选择,表现为植株越高、叶面积越大、花越多的个体雌性适合度越高;海拔最高（4 452 m）的种群中叶面积与花数的选择梯度接近显著。（3）植物性状分化伴随着海拔的变化而呈现出差异,较低海拔种群中花特征容易受到选择,而较高海拔种群中可能由于传粉者稀少、资源限制等因素使得株高、叶面积更容易受到选择。     

Genetic Architecture of Ear Fasciation in Maize (Zea mays) under QTL Scrutiny

Maize ear fasciation

Knowledge of the genes affecting maize ear inflorescence may lead to better grain yield modeling. Maize ear fasciation, defined as abnormal flattened ears with high kernel row number, is a quantitative trait widely present in Portuguese maize landraces.

Material and Methods

Using a segregating population derived from an ear fasciation contrasting cross (consisting of 149 F_2:3 families) we established a two location field trial using a complete randomized block design. Correlations and heritabilities for several ear fasciation-related traits and yield were determined. Quantitative Trait Loci (QTL) involved in the inheritance of those traits were identified and candidate genes for these QTL proposed.

Results and Discussion

Ear fasciation broad-sense heritability was 0.73. Highly significant correlations were found between ear fasciation and some ear and cob diameters and row number traits. For the 23 yield and ear fasciation-related traits, 65 QTL were identified, out of which 11 were detected in both environments, while for the three principal components, five to six QTL were detected per environment. Detected QTL were distributed across 17 genomic regions and explained individually, 8.7% to 22.4% of the individual traits or principal components phenotypic variance. Several candidate genes for these QTL regions were proposed, such as bearded-ear1, branched silkless1, compact plant1, ramosa2, ramosa3, tasselseed4 and terminal ear1. However, many QTL mapped to regions without known candidate genes, indicating potential chromosomal regions not yet targeted for maize ear traits selection.

Conclusions

Portuguese maize germplasm represents a valuable source of genes or allelic variants for yield improvement and elucidation of the genetic basis of ear fasciation traits. Future studies should focus on fine mapping of the identified genomic regions with the aim of map-based cloning.     

Relationship of runs of homozygosity with adaptive and production traits in a paternal broiler line

Genomic regions under high selective pressure present specific runs of homozygosity (ROH), which provide valuable information on the genetic mechanisms underlying the adaptation to environment imposed challenges. In broiler chickens, the adaptation to conventional production systems in tropical environments lead the animals with favorable genotypes to be naturally selected, increasing the frequency of these alleles in the next generations. In this study, ~1400 chickens from a paternal broiler line were genotyped with the 600 K Affymetrix® Axiom® high-density (HD) genotyping array for estimation of linkage disequilibrium (LD), effective population size (N_e), inbreeding and ROH. The average LD between adjacent single nucleotide polymorphisms (SNPs) in all autosomes was 0.37, and the LD decay was higher in microchromosomes followed by intermediate and macrochromosomes. The N_e of the ancestral population was high and declined over time maintaining a sufficient number of animals to keep the inbreeding coefficient of this population at low levels. The ROH analysis revealed genomic regions that harbor genes associated with homeostasis maintenance and immune system mechanisms, which may have been selected in response to heat stress. Our results give a comprehensive insight into the relationship between shared ROH regions and putative regions related to survival and production traits in a paternal broiler line selected for over 20 years. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the chicken genome.     

Allozyme variation of populations of Castanopsis carlesii (Fagaceae) revealing the diversity centres and areas of the greatest divergence in Taiwan

• Background and Aims The genetic variation and divergence estimated by allozyme analysis were used to reveal the evolutionary history of Castanopsis carlesii in Taiwan. Two major questions were discussed concerning evolutionary issues: where are the diversity centres, and where are the most genetically divergent sites in Taiwan?• Methods Twenty-two populations of C. carlesii were sampled throughout Taiwan. Starch gel electrophoresis was used to assay allozyme variation. Genetic parameters and mean F_ST values of each population were analysed using the BIOSYS-2 program. Mean F_ST values of each population against the remaining populations, considered as genetic divergence, were estimated using the FSTAT program.• Key Results Average values of genetic parameters describing the within-population variation, the average number of alleles per locus (A = 2·5), the effective number of alleles per locus (A_e = 1·38), the allelic richness (A_r = 2·38), the percentage of polymorphic loci (P = 69 %), and the expected heterozygosity (H_e = 0·270) were estimated. High levels of genetic diversity were found for C. carlesii compared with other local plant species. Genetic differentiation between populations was generally low.• Conclusions From the data of expected heterozygosity, one major diversity centre was situated in central Taiwan corroborating previous reports for other plant species. According to the mean F_ST value of each population, the most divergent populations were situated in two places. One includes populations located in north central Taiwan between 24·80°N and 24·20°N. The other is located in south-eastern Taiwan between 22·40°N and 23·10°N. These two regions are approximately convergent with the most divergent locations determined for several other plant species using chloroplast DNA markers published previously. An important finding obtained from this study is that unordered markers like allozymes can be used to infer past population histories as well as chloroplast DNA markers do.     

Balancing Selection for Pathogen Resistance Reveals an Intercontinental Signature of Red Queen Coevolution

The link between long-term host–parasite coevolution and genetic diversity is key to understanding genetic epidemiology and the evolution of resistance. The model of Red Queen host–parasite coevolution posits that high genetic diversity is maintained when rare host resistance variants have a selective advantage, which is believed to be the mechanistic basis for the extraordinarily high levels of diversity at disease-related genes such as the major histocompatibility complex in jawed vertebrates and R-genes in plants. The parasites that drive long-term coevolution are, however, often elusive. Here we present evidence for long-term balancing selection at the phenotypic (variation in resistance) and genomic (resistance locus) level in a particular host–parasite system: the planktonic crustacean Daphnia magna and the bacterium Pasteuria ramosa. The host shows widespread polymorphisms for pathogen resistance regardless of geographic distance, even though there is a clear genome-wide pattern of isolation by distance at other sites. In the genomic region of a previously identified resistance supergene, we observed consistent molecular signals of balancing selection, including higher genetic diversity, older coalescence times, and lower differentiation between populations, which set this region apart from the rest of the genome. We propose that specific long-term coevolution by negative-frequency-dependent selection drives this elevated diversity at the host''s resistance loci on an intercontinental scale and provide an example of a direct link between the host’s resistance to a virulent pathogen and the large-scale diversity of its underlying genes.     

The Genomic Impacts of Drift and Selection for Hybrid Performance in Maize

Although maize is naturally an outcrossing organism, modern breeding utilizes highly inbred lines in controlled crosses to produce hybrids. The U.S. Department of Agriculture’s reciprocal recurrent selection experiment between the Iowa Stiff Stalk Synthetic (BSSS) and the Iowa Corn Borer Synthetic No. 1 (BSCB1) populations represents one of the longest running experiments to understand the response to selection for hybrid performance. To investigate the genomic impact of this selection program, we genotyped the progenitor lines and >600 individuals across multiple cycles of selection using a genome-wide panel of ∼40,000 SNPs. We confirmed previous results showing a steady temporal decrease in genetic diversity within populations and a corresponding increase in differentiation between populations. Thanks to detailed historical information on experimental design, we were able to perform extensive simulations using founder haplotypes to replicate the experiment in the absence of selection. These simulations demonstrate that while most of the observed reduction in genetic diversity can be attributed to genetic drift, heterozygosity in each population has fallen more than expected. We then took advantage of our high-density genotype data to identify extensive regions of haplotype fixation and trace haplotype ancestry to single founder inbred lines. The vast majority of regions showing such evidence of selection differ between the two populations, providing evidence for the dominance model of heterosis. We discuss how this pattern is likely to occur during selection for hybrid performance and how it poses challenges for dissecting the impacts of modern breeding and selection on the maize genome.     

Recombinant near-isogenic lines: a resource for the mendelization of heterotic QTL in maize

Although heterosis is widely exploited in agriculture, a clear understanding of its genetic bases is still elusive. This work describes the development of maize recombinant near-isogenic lines (NILs) for the mendelization of six heterotic QTL previously identified based on a maize (Zea mays L.) RIL population. The efficient and inexpensive strategy adopted to generate sets of NILs starting from QTL-specific residual heterozygous lines (RHLs) is described and validated. In particular, we produced nine pairs of recombinant NILs for all six QTL starting from RHLs F_4:5 originally obtained during the production of the RIL population mentioned above. Whenever possible, two different NIL pairs were generated for each QTL. The efficiency of this procedure was tested by analyzing two segregating populations for two of the selected heterotic QTL for plant height, yield per plant and ears per plant. Both additive and dominant effects were observed, consistently with the presence of the QTL within the introgressed regions. Refinement of QTL detection was consistent with previous observations in terms of effects and position of the considered QTL. The genetic material developed in this work represents the starting point for QTL fine mapping aimed at understanding the genetic bases of hybrid vigor in maize. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic Divergence and Signatures of Natural Selection in Marginal Populations of a Keystone,Long-Lived Conifer,Eastern White Pine (Pinus strobus) from Northern Ontario

Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations are also expected to have lower genetic diversity and effective population size (N _e) and higher genetic differentiation than central populations. We tested these hypotheses using eastern white pine (Pinus strobus) as a model for keystone, long-lived widely-distributed plants. All 614 eastern white pine trees, in a complete census of two populations each of marginal old-growth, central old-growth, and central second-growth, were genotyped at 11 microsatellite loci. The central populations had significantly higher allelic and genotypic diversity, latent genetic potential (LGP) and N _e than the marginal populations. However, heterozygosity and fixation index were similar between them. The marginal populations were genetically diverged from the central populations. Model testing suggested predominant north to south gene flow in the study area with curtailed gene flow to northern marginal populations. Signatures of natural selection were detected at three loci in the marginal populations; two showing divergent selection with directional change in allele frequencies, and one balancing selection. Contrary to the general belief, no significant differences were observed in genetic diversity, differentiation, LGP, and N _e between old-growth and second-growth populations. Our study provides information on the dynamics of migration, genetic drift and selection in central versus marginal populations of a keystone long-lived plant species and has broad evolutionary, conservation and adaptation significance.     

Species Persistence with Hybridization in Toad-Headed Lizards Driven by Divergent Selection and Low Recombination

Speciation plays a central role in evolutionary studies, and particularly how reproductive isolation (RI) evolves. The origins and persistence of RI are distinct processes that require separate evaluations. Treating them separately clarifies the drivers of speciation and then it is possible to link the processes to understand large-scale patterns of diversity. Recent genomic studies have focused predominantly on how species or RI originate. However, we know little about how species persist in face of gene flow. Here, we evaluate a contact zone of two closely related toad-headed lizards (Phrynocephalus) using a chromosome-level genome assembly and population genomics. To some extent, recent asymmetric introgression from Phrynocephalus putjatai to P. vlangalii reduces their genomic differences. However, their highly divergent regions (HDRs) have heterogeneous distributions across the genomes. Functional gene annotation indicates that many genes within HDRs are involved in reproduction and RI. Compared with allopatric populations, contact areas exhibit recent divergent selection on the HDRs and a lower population recombination rate. Taken together, this implies that divergent selection and low genetic recombination help maintain RI. This study provides insights into the genomic mechanisms that drive RI and two species persistence in the face of gene flow during the late stage of speciation.     

Fine mapping a major QTL for kernel number per row under different phosphorus regimes in maize (Zea mays L.)

Phosphorus (P) is one of the essential macronutrients for plant growth and development. Grain yield is the primary trait of interest in maize breeding programs. Maize grain yield and yield-related traits are seriously affected by P deficiency. Kernel number per row (KN), as one of the major components of grain yield, has attracted the attention of more and more breeders. In our previous study, one major QTL (named qKN), controlling KN under different P regimes was mapped to the interval between molecular markers bnlg1360 and umc1645 on chromosome 10 using a F _2:3 population derived from the cross between maize inbreds 178 and 5,003 (107). In order to understand its genetic basis, we developed a population of near isogenic lines (NILs) and two P regimes were used to fine map and characterize qKN. The QTL qKN was finally localized in a region of ~480 kb. A single qKN allele of inbred 178 increased KN by 6.08–10.76 % in the 5,003 (107) background; qKN acted in a partially dominant manner. Our results will be instrumental for the future identification and isolation of the candidate gene underlying qKN. The tightly linked molecular markers that we developed for qKN will be useful in maize breeding programs for improving KN applying the marker-assisted selection.     

Identification of quantitative trait loci for nitrogen use efficiency in maize

Intensively managed crop systems are normally dependent on nitrogen input to maximize yield potential. Improvements in nitrogen- use efficiency (NUE) in crop plants may support the development of cropping systems that are more economically efficient and environment friendly. The objective of this study was to map and characterize quantitative trait loci (QTL) for NUE in a maize population. In preliminary experiments, inbred lines contrasting for NUE were identified and were used to generate populations of F2:3 families for genetic study. A total of 214 F2:3 families were evaluated in replicated trials under high nitrogen (280 kg/ha) and low nitrogen (30 kg/ha) conditions in 1996 and 1997. Analysis of ear-leaf area, plant height, grain yield, ears per plant, kernels number per ear, and kernel weight indicated significant genetic variation among F2:3 families. The heritability of these traits was found to be high (h2=0.57–0.81). The mapping population were genotyped using a set of 99 restriction fragment length polymorphism (RFLP) markers. A linkage map of these markers was developed and used to identify QTL. Between two and six loci were found to be associated with each trait. The correspondence of several genomic regions with traits measured under nitrogen limited conditions suggests the presence of QTL associated with NUE. QTLs will help breeders to improve their maize ideotype of a low-nitrogen efficiency by identifying those constitutive and adaptive traits involved in the expression of traits significantly correlated with yield, such as ear leaf area and number of ears per plant. This revised version was published online in June 2006 with corrections to the Cover Date.     

Selection for uniformity in livestock by exploiting genetic heterogeneity of residual variance

In some situations, it is worthwhile to change not only the mean, but also the variability of traits by selection. Genetic variation in residual variance may be utilised to improve uniformity in livestock populations by selection. The objective was to investigate the effects of genetic parameters, breeding goal, number of progeny per sire and breeding scheme on selection responses in mean and variance when applying index selection. Genetic parameters were obtained from the literature. Economic values for the mean and variance were derived for some standard non-linear profit equations, e.g. for traits with an intermediate optimum. The economic value of variance was in most situations negative, indicating that selection for reduced variance increases profit. Predicted responses in residual variance after one generation of selection were large, in some cases when the number of progeny per sire was at least 50, by more than 10% of the current residual variance. Progeny testing schemes were more efficient than sib-testing schemes in decreasing residual variance. With optimum traits, selection pressure shifts gradually from the mean to the variance when approaching the optimum. Genetic improvement of uniformity is particularly interesting for traits where the current population mean is near an intermediate optimum.     

Chemical Variation in a Dominant Tree Species: Population Divergence,Selection and Genetic Stability across Environments

Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E). We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs) in a dominant tree species, Eucalyptus globulus. Using two common garden trials we examined variation in PSMs at multiple genetic scales; among 12 populations covering the full geographic range of the species and among up to 60 families within populations. Significant genetic variation in the expression of many PSMs resides both among and within populations of E. globulus with moderate (e.g., sideroxylonal A h²op = 0.24) to high (e.g., macrocarpal G h²op = 0.48) narrow sense heritabilities and high coefficients of additive genetic variation estimated for some compounds. A comparison of Qst and Fst estimates suggest that variability in some of these traits may be due to selection. Importantly, there was no genetic by environment interaction in the expression of any of the quantitative chemical traits despite often significant site effects. These results provide evidence that natural selection has contributed to population divergence in PSMs in E. globulus, and identifies the formylated phloroglucinol compounds (particularly sideroxylonal) and a dominant oil, 1,8-cineole, as candidates for traits whose genetic architecture has been shaped by divergent selection. Additionally, as the genetic differences in these PSMs that influence community phenotypes is stable across environments, the role of plant genotype in structuring communities is strengthened and these genotypic differences may be relatively stable under global environmental changes.     

Post-Domestication Selection in the Maize Starch Pathway

Modern crops have usually experienced domestication selection and subsequent genetic improvement (post-domestication selection). Chinese waxy maize, which originated from non-glutinous domesticated maize (Zea mays ssp. mays), provides a unique model for investigating the post-domestication selection of maize. In this study, the genetic diversity of six key genes in the starch pathway was investigated in a glutinous population that included 55 Chinese waxy accessions, and a selective bottleneck that resulted in apparent reductions in diversity in Chinese waxy maize was observed. Significant positive selection in waxy (wx) but not amylose extender1 (ae1) was detected in the glutinous population, in complete contrast to the findings in non-glutinous maize, which indicated a shift in the selection target from ae1 to wx during the improvement of Chinese waxy maize. Our results suggest that an agronomic trait can be quickly improved into a target trait with changes in the selection target among genes in a crop pathway.     

Selection for litter size in pigs. II. Efficiency of closed and open selection lines*

A selection experiment on litter size in the pig was carried on for seventeen generations in an Inra experimental herd. The founder population was made up of 10 males and 120 females from the Large White breed. Selection was first performed for ten generations in a closed line, compared to a control line derived from the same founder population. Selection was carried on within sire family on the total number of piglets born in the first two litters of the dam (TB1 + TB2). After ten generations, the selection criterion became dam TB1 only. The control line was then discontinued and a panel of frozen semen from the 11th generation boars was created for later comparisons. The selected line was opened to gilt daughters of hyperprolific boars and sows, at a rate of 1/8 per generation, and the same selection procedure was applied irrespective of the origin of the gilt. During the whole experiment, the number of ova shed (OS) and the number of live embryos (LE) at 30 days in the 3rd pregnancy were recorded. These two parts of the experiment were analysed using REML estimation of genetic parameters and a BLUP-Animal Model in order to estimate the responses to selection. Significant heritabilities for TB1, TB2, OS and LE were obtained, i.e. 0.10, 0.05, 0.43 and 0.19, respectively. Significant common environment variances and covariances were estimated for nearly all traits. Significantly positive BLUP responses per generation were observed from G0 to G17 for TB1 (+0.086), TB2 (+0.078), OS (+0.197) and LE (+0.157). However, the responses were 3- to 4-fold higher in the G12–G17 interval compared to G0–G11, and they were also in fair agreement with previous estimates based on standard least-squares procedures, using the control line and the control frozen semen panel. Since G11, the selection intensity was increased by nearly 80 p. cent compared to the previous generations, and the proportion of hyperprolific ancestry increased up to 65 p. cent in the sows of the last generation. The total genetic gain of about 1.4 piglets at birth per litter could be shared between a gain due to immigration, of about 0.8 piglets per litter, and a within-line selection gain of about 0.6 piglets. Thus by combining selection and immigration in the second part of the experiment, advantage could be taken from both the genetic superiority of the immigrants and the higher internal selection intensity made possible by immigration.