Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

Genetics and analysis of quantitative traits

▪ Abstract We hypothesize that the evolutionary potential of a pathogen population is reflected in its population genetic structure. Pathogen populations with a high evolutionary potential are more likely to overcome genetic resistance than pathogen populations with a low evolutionary potential. We propose a flexible framework to predict the evolutionary potential of pathogen populations based on analysis of their genetic structure. According to this framework, pathogens that pose the greatest risk of breaking down resistance genes have a mixed reproduction system, a high potential for genotype flow, large effective population sizes, and high mutation rates. The lowest risk pathogens are those with strict asexual reproduction, low potential for gene flow, small effective population sizes, and low mutation rates. We present examples of high-risk and low-risk pathogens. We propose general guidelines for a rational approach to breed durable resistance according to the evolutionary potential of the pathogen.

Pathogen population genetics, evolutionary potential, and durable resistance

This review of Fusarium ear blight (scab) of small grain cereals has shown that up to 17 causal organisms have been associated with the disease, which occurs in most cereal-growing areas of the world. The most common species were Fusarium graminearum (Gibberella zeae), F. culmorum, F, avenaceum (G, avenacea), F, poae and Microdochium nivale (Monographella nivalis). The disease was recorded most frequently under hot, wet climatic conditions where significant yield losses and mycotoxin accumulation in grain were reported. Possible sources of inoculum were reported as crop debris, alternative hosts and Fusarium seedling blight and foot rot of cereals. The mode of dispiersal of inoculum to ears remains unclear, but contaminated arthropod vectors, systemic fungal growth through plants, and wind and rain-splash dispersal of spores have been proposed. Infection of wheat ears was shown to occur mainly during anthesis, and it has been demonstrated that fungal growth stimulants may be present in anthers. Despite the importance of the disease, particularly during epidemic years, control methods are limited. Much effort has gone into breeding resistant wheat varieties and into improving our understanding of the possible mechanisms and genetic basis of resistance, with only moderate success. There are also surprisingly few reports of successful fungicidal or biological control of the disease in the field.

Fusarium ear blight (scab) in small grain cereals—a review

In the last three to five years, doubled hap- loid (DH) lines have increasingly been used in maize (Zea mays L.) research and breeding. This became possi- ble by substantial progress in the in vivo haploid induc- tion technology. Herein, we describe the development and characteristics of a new induction line, RWS, and dis- cuss quantitative genetic and logistic aspects of the use of DH lines in hybrid maize breeding. - Induction line RWS was derived from an F 5 plant of a cross between the Russian induction synthetic KEMS and the French induc- tion line WS14. Kernels with a haploid or F 1 embryo can be distinguished by means of the expression of the domi- nant anthocyanin marker gene R1-nj. Misclassification rates based on this marker gene are generally low except for donors carrying anthocyanin inhibitor genes. Reliable estimates of the induction rate were obtained by using tester genotypes with recessive morphological markers. In tests across various induction environments, RWS consis- tently showed the highest induction rate (8.1% on aver- age) compared to other inducers evaluated herein. - Ad- vantages of using DH lines in hybrid breeding include (1) maximum genetic variance in line per se and testcross tri- als, (2) high reproducibility of early-selection results, (3) high efficiency in stacking targeted gene arrangements and (4) simplified logistics. High cost-savings are possible due to reduced expenses for the selfing program, han- dling and shipping of seed batches, and for maintenance breeding. Moreover, outstanding DH lines may be pro- tected and commercialized several seasons earlier than lines developed by inbreeding.

In vivo haploid induction in maize - performance of new inducers and significance of doubled haploid lines in hybrid breeding

The stay-green trait is a reported component of tolerance to terminal drought stress in sorghum. To map quantitative trait loci (QTLs) for stay-green, two sorghum recombinant inbred populations (RIPs) of 226 F3:5 lines each were developed from crosses (1) IS9830 × E36-1 and (2) N13 × E36-1. The common parental line, E36-1 of Ethiopian origin, was the stay-green trait source. The genetic map of RIP 1 had a total length of 1,291 cM, with 128 markers (AFLPs, RFLPs, SSRs and RAPDs) distributed over ten linkage groups. The map of RIP 2 spanned 1,438 cM and contained 146 markers in 12 linkage groups. The two RIPs were evaluated during post-rainy seasons at Patancheru, India, in 1999/2000 (RIP 2) and 2000/2001 (RIP 1). The measures of stay-green mapped were the green leaf area percentages at 15, 30 and 45 days after flowering (% GL15, % GL30 and % GL45, respectively). Estimated repeatabilities for % GL15, % GL30 and % GL45 amounted to 0.89, 0.81 and 0.78 in RIP 1, and 0.91, 0.88 and 0.85 in RIP 2, respectively. The number of QTLs for the three traits detected by composite interval mapping ranged from 5 to 8, explaining 31% to 42% of the genetic variance. In both RIPs, both parent lines contributed stay-green alleles. Across the three measures of the stay-green trait, three QTLs on linkage groups A, E and G were common to both RIPs, with the stay-green alleles originating from E36-1. These QTLs were therefore consistent across the tested genetic backgrounds and years. After QTL validation across sites and verification of the general benefit of the stay-green trait for grain yield performance and stability in the target areas, the corresponding chromosomal regions could be candidates for marker-assisted transfer of stay-green into elite materials.

/pdf/qtl-mapping-of-stay-green-in-two-sorghum-recombinant-inbred-188bzb230c.pdf

QTL mapping of stay-green in two sorghum recombinant inbred populations

Improved methodologies for breeding striga-resistant sorghums

Maize (Zea mays L.) cultivars with improved N-use efficiency would be beneficial for low-input production systems. Our objective was to estimate quantitative genetic parameters to optimize breeding programs for improving productivity under low N levels. Results of 21 field experiments with European breeding materials belonging to the flint and dent gene pool are presented. The study was performed during 1989 and 1999 at several locations in typical maize growing regions of Germany and France. All experiments were conducted at high (HN) and low (LN, no N fertilizer applied) N levels. Average grain yield was reduced by 37% at LN compared with HN. Coefficients of genotypic correlation between HN and LN were variable with an average of r G = 0.74 for grain yield and generally high for grain dry matter content. For grain yield, analyses of variance were computed from relative data, where plot values were expressed as percentage of the trial mean. Variances caused by genotype (G), G x location (L) interaction, and error effects were higher at LN compared with HN, with similar heritabilities at both N levels. For the untransformed data, components of variance were higher at HN than at LN. Genotype x N as well as G x L x N level interaction variances were significant in most experiments. Efficiency of improvement of grain yield at LN through indirect selection at HN was 70% compared with direct selection at LN. A trend toward increased efficiency of direct selection under LN conditions was evident with decreasing grain yield at LN.

Improving Nitrogen-Use Efficiency in European Maize

Turcicum or northern corn leaf blight (NCLB) incited by the ascomycete Setosphaeria turcica, anamorph Exserohilum turcicum, is a ubiquitous foliar disease of maize. Diverse sources of qualitative and quantitative resistance are available but qualitative resistances (Ht genes) are often unstable. In the tropics especially, they are either overcome by new virulent races or they suffer from climatically sensitive expression. Quantitative resistance is expressed independently of the physical environment and has never succumbed to S. turcica pathotypes in the field. This review emphasizes the identification and mapping of genes related to quantitative NCLB resistance. We deal with the consistency of the genomic positions of quantitative trait loci (QTL) controlling resistance across different maize populations, and with the clustering of genes for resistance to S. turcica and other fungal pathogens or insect pests in the maize genome. Implications from these findings for further genomic research and resistance breeding are drawn.

Incubation period (IP) and area under the disease progress curve (AUDPC), based on multiple disease ratings, are important component traits of quantitative NCLB resistance. They are generally tightly correlated (rp≅ 0.8) and highly heritable (h2≅ 0.75). QTL for resistance to NCLB (IP and AUDPC) were identified and characterized in three mapping populations (A, B, C). Population A, a set of 121-150 F3 families of the cross B52×mo17, represented US Corn Belt germplasm with a moderate level of resistance. It was field-tested in Iowa, USA, and Kenya, and genotyped at 112 restriction fragment length polymorphism (RFLP) loci. Population B consisted of 194-256 F3 families of the cross Lo951×CML202, the first parent being a Corn-Belt-derived European inbred line and the second parent being a highly resistant tropical African inbred line. The population was also tested in Kenya and genotyped with 110 RFLP markers. Population C was derived from a cross between two early-maturing European inbred lines, D32 and D145, both having a moderate level of resistance. A total of 220 F3 families were tested in Switzerland and characterized with 87 RFLP and seven SSR markers. In each of the three studies, 12-13 QTL were detected by composite interval mapping at a signifcance threshold of LOD=2.5. The phenotypic and the genotypic variance were explained to an extent of 50-70% and 60-80%, respectively. Gene action was additive to partly dominant, as in previous generation means and combining ability analyses with other genetic material. In each population, gene effects of the QTL were of similar magnitude and no putative major genes were discovered. QTL for AUDPC were located on chromosomes 1 to 9. All three populations carried QTL in identical genomic regions on chromosomes 3 (bin 3.06/07), 5 (bin 3.06/07) and 8 (bin 8.05/06). The major genes Ht2 and Htn1 were also mapped to bins 8.05 and 8.06, suggesting the presence of a cluster of closely linked major and minor genes. The chromosomal bins 3.05, 5.04 and 8.05, or adjacent intervals, were further associated with QTL and major genes for resistance to eight other fungal diseases and insect pests of maize. Bins 1.05/07 and 9.05 were found to carry population-specifc genes for resistance to S. turcica and other organisms. Several disease lesion mimic mutations, resistance gene analogues and genes encoding pathogenesis-related proteins were mapped to regions harbouring NCLB resistance QTL.

Hartwig H. Geiger

Papers

In vivo haploid induction in maize - performance of new inducers and significance of doubled haploid lines in hybrid breeding

QTL mapping of stay-green in two sorghum recombinant inbred populations

Improved methodologies for breeding striga-resistant sorghums

Improving Nitrogen-Use Efficiency in European Maize

Genes for resistance to northern corn leaf blight in diverse maize populations