Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize

A new genetic map of maize, ISU-IBM Map4, that integrates 2029 existing markers with 1329 new indel polymorphism (IDP) markers has been developed using intermated recombinant inbred lines (IRILs) from the intermated B73xMo17 (IBM) population. The website http://magi.plantgenomics.iastate.edu provides access to IDP primer sequences, sequences from which IDP primers were designed, optimized marker-specific PCR conditions, and polymorphism data for all IDP markers. This new gene-based genetic map will facilitate a wide variety of genetic and genomic research projects, including map-based genome sequencing and gene cloning. The mosaic structures of the genomes of 91 IRILs, an important resource for identifying and mapping QTL and eQTL, were defined. Analyses of segregation data associated with markers genotyped in three B73/Mo17-derived mapping populations (F2, Syn5, and IBM) demonstrate that allele frequencies were significantly altered during the development of the IBM IRILs. The observations that two segregation distortion regions overlap with maize flowering-time QTL suggest that the altered allele frequencies were a consequence of inadvertent selection. Detection of two-locus gamete disequilibrium provides another means to extract functional genomic data from well-characterized plant RILs.     

Genetic diversity of maize inbred lines within and among heterotic groups revealed by RFLPs

Summary The objectives of this study were (1) to investigate genetic diversity for RFLPs in a set of important maize inbreds commonly used in Italian breeding programs, (2) to compare genetic similarities between unrelated lines from the same and different heterotic groups, and (3) to examine the potential of RFLPs for assigning maize inbreds to heterotic groups. Forty inbreds were analyzed for RFLPs with two restriction enzymes (EcoRI and HindIII) and 82 DNA clones uniformly distributed over the maize genome. Seventy clone-enzyme combinations gave single-banded RFLP patterns, and 79 gave multiple-banded RFLP patterns. The average number of RFLP patterns detected per clone-enzyme combination across all inbreds was 5.8. RFLP data revealed a wide range of genetic diversity within the two heterotic groups assayed, Iowa Stiff Stalk Synthetic (BSSS) and Lancaster Sure Crop (LSC). Genetic similarity (GS) between lines was estimated from binary RFLP data according to the method of Nei and Li (1979). The mean GS for line combinations of type BSSS × LSC (0.498) was substantially smaller than for unrelated line combinations or type BSSS × BSSS (0.584) but almost as great as for un-related line combinations of type LSC × LSC (0.506). Principal coordinate and cluster analyses based on GS values resulted in the separate groupings of lines, which is consistent with known pedigree information. A comparison between both methods for multivariate analyses of RFLP data is presented.     

Patterns of genomic variation in Chinese maize inbred lines and implications for genetic improvement

Key message

Genetic relationships among Chinese maize germplasms reveal historical trends in heterotic patterns from Chinese breeding programs and identify line Dan340 as a potential genome donor for elite inbred line Zheng58.

Abstract

The characterization of the genetic relationships, heterotic patterns and breeding history of lines in maize breeding programs allows breeders to efficiently use maize germplasm for line improvement over time. In this study, 269 temperate inbred lines, most of which have been widely used in Chinese maize breeding programs since the 1970s, were genotyped using the Illumina MaizeSNP50 BeadChip, which contains 56,110 single-nucleotide polymorphisms. The STRUCTURE analysis, cluster analysis and principal coordinate analysis results consistently revealed seven groups, of which five were consistent with known heterotic groups within the Chinese maize germplasm—Domestic Reid, Lancaster, Zi330, Tang SPT and Tem-tropic I (also known as “P”). These genetic relationships also allowed us to determine the historical trends in heterotic patterns during the three decades from 1970 to 2000, represented by Mo17 from Lancaster, HuangZaoSi (HZS) from Tang SPT, Ye478 from Domestic Reid and P178 from Tem-tropic I heterotic groups. Mo17-related commercial hybrids were widely used in the 1970s and 1980s, followed by the release of HZS- and Ye478-related commercial hybrids in the 1980s and 1990s, and the introduction of Tem-tropic I group in the 1990s and 2000s. Additionally, we identified inbred line Dan340 as a potential genome donor for Zheng58, which is the female parent of the most widely grown commercial hybrid ZhengDan958 in China. We also reconstructed the recombination events of elite line HZS and its 14 derived lines. These findings provide useful information to direct future maize breeding efforts.

     

SSR analysis of genetic diversity among maize inbred lines adapted to cold regions of Japan

Information regarding diversity and relationships among breeding material is necessary for hybrid maize (Zea mays L.) breeding. Simple-sequence repeat (SSR) analysis of the 60 loci distributed uniformly throughout the maize genome was carried out for 65 inbred lines adapted to cold regions of Japan in order to assess genetic diversity among the inbred lines and to assign them to heterotic groups. The mean value (0.69) of the polymorphic-index content (PIC) for the SSR loci provided sufficient discrimination-ability for the assessment of genetic diversity among the inbred lines. The correlation between the genetic-similarity (GS) estimates and the coancestry coefficient was significant (r = 0.70). The average-linkage (UPGMA) cluster analysis and principal-coordinate analysis (PCOA) for a matrix of the GS estimates showed that the Northern flint inbred lines bred in Japan were similar to a Canadian Northern flint inbred line CO12 and a European flint inbred line F283, and that dent inbred lines bred in Japan were similar to BSSS inbred lines such as B73. These associations correspond to the known pedigree records of these inbred lines. The results indicate that SSR analysis is effective for the assessment of genetic diversity among maize inbred lines and for the assignment of inbred lines to heterotic groups.     

Classical genetic and quantitative trait loci analyses of heterosis in a maize hybrid between two elite inbred lines

The exploitation of heterosis is one of the most outstanding advancements in plant breeding, although its genetic basis is not well understood yet. This research was conducted on the materials arising from the maize single cross B73 x H99 to study heterosis by procedures of classical genetic and quantitative trait loci (QTL) analyses. Materials were the basic generations, the derived 142 recombinant inbred lines (RILs), and the three testcross populations obtained by crossing the 142 RILs to each parent and their F(1). For seedling weight (SW), number of kernels per plant (NK), and grain yield (GY), heterosis was >100% and the average degree of dominance was >1. Epistasis was significant for SW and NK but not for GY. Several QTL were identified and in most cases they were in the additive-dominance range for traits with low heterosis and mostly in the dominance-overdominance range for plant height (PH), SW, NK, and GY. Only a few QTL with digenic epistasis were identified. The importance of dominance effects was confirmed by highly significant correlations between heterozygosity level and phenotypic performance, especially for GY. Some chromosome regions presented overlaps of overdominant QTL for SW, PH, NK, and GY, suggesting pleiotropic effects on overall plant vigor.     

Uptake and distribution of cadmium in maize inbred lines

Genotypic variation in uptake and distribution of cadmium (Cd) was studied in 19 inbred lines of maize (Zea mays L.). The inbred lines were grown for 27 days on an in situ Cd-contaminated sandy soil or for 20 days on nutrient solution culture with 10 µg Cd L^-1. The Cd concentrations in the shoots showed large genotypic variation, ranging from 0.9 to 9.9 µg g^-1 dry wt. for the Cd-contaminated soil and from 2.5 to 56.9 µg g^-1 dry wt. for the nutrient solution culture. The inbred lines showed a similar ranking for the Cd concentrations in the shoots for both growth media (r²=0.89). Two main groups of inbreds were distinguished: a group with low shoot, but high root Cd concentrations (shoot: 7.4±5.3 µg g^-1 dry wt.; root: 206.0±71.2 µg g^-1 dry wt.; shoot Cd excluder) and a group with similar shoot and root Cd concentrations (shoot: 54.2±3.4 µg g^-1 dry wt.; root: 75.6±11.2 µg g^-1 dry wt.; non-shoot Cd excluder). The classification of the maize inbred lines and the near equal whole-plant Cd uptake between the two groups demonstrates that internal distribution rather than uptake is causing the genotypic differences in shoot Cd concentration of maize inbred lines. Zinc (Zn), a micronutrient chemically related to Cd, showed an almost similar distribution pattern for all maize inbred lines. The discrepancy in the internal distribution between Cd and Zn emphasizes the specificity of the Cd distribution in maize inbred lines.     

Quality control genotyping for assessment of genetic identity and purity in diverse tropical maize inbred lines

Quality control (QC) genotyping is an important component in breeding, but to our knowledge there are not well established protocols for its implementation in practical breeding programs. The objectives of our study were to (a) ascertain genetic identity among 2–4 seed sources of the same inbred line, (b) evaluate the extent of genetic homogeneity within inbred lines, and (c) identify a subset of highly informative single-nucleotide polymorphism (SNP) markers for routine and low-cost QC genotyping and suggest guidelines for data interpretation. We used a total of 28 maize inbred lines to study genetic identity among different seed sources by genotyping them with 532 and 1,065 SNPs using the KASPar and GoldenGate platforms, respectively. An additional set of 544 inbred lines was used for studying genetic homogeneity. The proportion of alleles that differed between seed sources of the same inbred line varied from 0.1 to 42.3?%. Seed sources exhibiting high levels of genetic distance are mis-labeled, while those with lower levels of difference are contaminated or still segregating. Genetic homogeneity varied from 68.7 to 100?% with 71.3?% of the inbred lines considered to be homogenous. Based on the data sets obtained for a wide range of sample sizes and diverse genetic backgrounds, we recommended a subset of 50–100 SNPs for routine and low-cost QC genotyping, verified them in a different set of double haploid and inbred lines, and outlined a protocol that could be used to minimize errors in genetic analyses and breeding.     

Comparison of whole-genome prediction models for traits with contrasting genetic architecture in a diversity panel of maize inbred lines

ABSTRACT: BACKGROUND: There is increasing empirical evidence that whole-genome prediction (WGP) is a powerful tool for predicting line and hybrid performance in maize. However, there is a lack of knowledge about the sensitivity of WGP models towards the genetic architecture of the trait. Whereas previous studies exclusively focused on highly polygenic traits, important agronomic traits such as disease resistances, nutrifunctional or climate adaptational traits have a genetic architecture which is either much less complex or unknown. For such cases, information about model robustness and guidelines for model selection are lacking. Here, we compared five WGP models with different assumptions about the distribution of the underlying genetic effects. As contrasting model traits, we chose three highly polygenic agronomic traits and three metabolites each with a major QTL explaining 22 to 30 % of the genetic variance in a panel of 289 diverse maize inbred lines genotyped with 56,110 SNPs. RESULTS: We found the five WGP models to be remarkable robust towards trait architecture with the largest differences in prediction accuracies ranging between 0.05 and 0.14 for the same trait, most likely as the result of the high level of linkage disequilibrium prevailing in elite maize germplasm. Whereas RR-BLUP performed best for the agronomic traits, it was inferior to LASSO or elastic net for the three metabolites. We found the approach of genome partitioning of genetic variance, first applied in human genetics, as useful in guiding the breeder which model to choose, if prior knowledge of the trait architecture is lacking. CONCLUSIONS: Our results suggest that in diverse germplasm of elite maize inbred lines with a high level of LD, WGP models differ only slightly in their accuracies, irrespective of the number and effects of QTL found in previous linkage or association mapping studies. However, small gains in prediction accuracies can be achieved if the WGP model is selected according to the genetic architecture of the trait. If the trait architecture is unknown e.g. for novel traits which only recently received attention in breeding, we suggest to inspect the distribution of the genetic variance explained by each chromosome for guiding model selection in WGP.     

Performance prediction of F1 hybrids between recombinant inbred lines derived from two elite maize inbred lines

Selection of recombinant inbred lines (RILs) from elite hybrids is a key method in maize breeding especially in developing countries. The RILs are normally derived by repeated self-pollination and selection. In this study, we first investigated the accuracy of different models in predicting the performance of F₁ hybrids between RILs derived from two elite maize inbred lines Zong3 and 87-1, and then compared these models through simulation using a wider range of genetic models. Results indicated that appropriate prediction models depended on genetic architecture, e.g., combined model using breeding value and genome-wide prediction (BV+GWP) has the highest prediction accuracy for high V _D/V _A ratio (>0.5) traits. Theoretical studies demonstrated that different components of genetic variance were captured by different prediction models, which in turn explained the accuracy of these models in predicting the F₁ hybrid performance. Based on genome-wide prediction model (GWP), 114 untested F₁ hybrids possibly having higher grain yield than the original F₁ hybrid Yuyu22 (the single cross between Zong3 and 87-1) have been identified and recommended for further field test.     

A broad range of Fab stabilities within a host of therapeutic IgGs

Although the functional properties of IgGs are well known, little has been published concerning the stability of whole IgG molecules. Stability is, however, a requirement for the development of antibodies for therapeutic or diagnostic applications. The hypervariable antigen-binding region (Fv) is responsible for stability variations between IgGs of identical subclass. To determine the range of stabilities that may be expected for human(ized) antibodies, differential scanning calorimetry was performed on 17 human(ized) antibodies from various in-house programs. The antigen-binding fragments (Fabs) of these antibodies exhibited thermal unfolding transitions with midpoints (T(M)s) varying from 57 to 82 degrees C. Antibodies with very low Fab stabilities were found to aggregate and express poorly. Fab instability was often associated with high levels of uncommonly observed amino acids or CDR loop lengths particularly within the variable heavy chain domain. Overall, the study provides a thermostability range for IgGs and suggests possible stability guidelines for developing antibody diagnostics or therapeutics.     

影响农杆菌介导玉米优良自交系遗传转化的因素

以我国玉米骨干自交系9046,齐319,414,Mo17的幼胚为材料,在已经建立的农杆菌介导的玉米幼胚转化体系的基础上,研究了影响农杆菌介导玉米优良自交系遗传转化的因素,建立了优化的玉米优良自交系的遗传转化体系。研究结果表明,1．0—2．0mm的玉米幼胚是最适宜的转化受体;在感染液和共培养基中都加入乙酰丁香酮(200μmol／L)和抗坏血酸(50mg／L),能显著提高农杆菌对玉米的侵染能力;而感染前将幼胚高渗透压预处理未能提高转化率;延迟筛选有利于提高抗性愈伤组织的存活率。应用优化后的转化体系,获得了这4个玉米优良自交系的转基因植株,PCR阳性植株率为1．71％-4．09％。转化植株叶片总DNA的PCR和Southern杂交分析表明,T-DNA上的外源基因已经整合进了玉米基因组,并且在大多数转基因植株(71．4％)中为单位点插入。这一体系的建立,为进一步将有用基因导入玉米优良自交系奠定了基础。     

Effect of selection on the heterozygosity of inbred lines of maize

Although pedigree selection is the most commonly used method for developing inbred lines of maize, there are no studies on its effect on the heterozygosity of the lines. The objective of this work was to study the effect of pedigree selection on their heterozygosity. Thirteen F₅ or F₆ maize inbred lines developed by the pedigree selection method in four breeding programs and their F₁ and F₂ − F₄ ancestors were genotyped with simple sequence repeat markers distributed along the genome. Simulation was also conducted assuming different models of selection to investigate the selective forces needed to explain the data. In the F₂, F₃ and F₄ 40%, 66% and 86% of the markers segregating in the F₁ were fixed; that is, in the F₂ and F₃ fixation was lower than neutral expectation, but higher in the F₄. Due to such opposite apparent directions of selection, the heterozygosity of the lines in the F₅ or F₆ generations did not differ significantly from neutral expectations. The time to fixation differed from that expected with neutrality for most of the chromosomes, indicating that selection is distributed across the genome; but apparent overdominant effects in chromosome 7 were higher than in other chromosomes. In conclusion, the relationship between heterozygosity and vigour may reduce the effectiveness of pedigree selection in its goal of selecting the more vigorous, homozygous individuals. A more effective procedure is proposed using molecular markers for the identification of the more homozygous individuals, the most vigorous of those individuals being selected.     

Agronomic evaluation of inbred lines derived from tissue cultures of maize

Summary Tissue culture-induced variation has been proposed as a novel source of variation for crop improvement. In maize (Zea mays L.), chromosome aberrations and qualitative genetic variants have been induced during in vitro culture. The proportion of regenerated plants carrying such variants has been shown to increase with culture age. The objective of this research was to evaluate the relationship between culture age and somaclonal variation for several agronomic traits. Six sib-pollinated ears of S₀ (F₂) plants in four OH43 ms/A188 populations each provided control seed and embryos for culture initiation. S₂ lines derived from control seed and from plants regenerated 4 and 8 months after culture initiation were grouped according to their source ear and grown in 6 separate trials. A total of 305 tissue culture-derived and 48 control lines were evaluated as lines per se and in a testcross at each of three locations. Tissue culturederived lines and their testcrosses generally had lower grain yield and moisture. Since grain yield and moisture were not positively correlated in any trial, the highest yielding lines could be selected without increasing grain moisture. Grain yield and plant height tended to decrease with culture age. Although tissue culture-derived lines were, on average, inferior, the highest yielding line per se in three of six trials and the top-ranked line in five of six trials for yield and moisture were derived from tissue culture. The results indicate that tissue culture may generate variation for agronomic traits. Some of the variation, particularly the trend towards earlier maturity, could be useful. However, this method may require screening large populations because of the tendency to generate a large proportion of inferior lines.Contribution from Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108. Minnesota Agric. Exp. Stn. Scientific Journal Series Paper No. 15,172     

Analyses of genetic diversity among maize inbred lines differing for resistance to pink borer and post-flowering stalk rot

Identification of the diverse sources of resistance is an important issue among the breeders for developing pest and disease free hybrids, to reduce the inoculum load, to prolong the life of inbred lines/hybrids and to reduce the cost of cultivation. Molecular diversity analysis was carried out among 23 maize inbred lines with respect to post flowering stalk rot and pink borer. Forty six SSR markers were employed among eight post flowering stalk rot (PFSR) and seven pink borer resistant lines along with eight other inbred lines to identify diverse resistant sources for developing resistant heterotic combinations to above pests and diseases. Number of alleles per SSR marker ranged from 2 to 9 averaging 4.11. The polymorphism information content (PIC) ranged from 0.272 to 0.839 with an average of 0.568. Discrimination rate (DR) of the markers ranged from 0.095 to 0.861 with a mean of 0.618. Number of alleles was highly correlated with PIC and DR. The pair-wise genetic dissimilarity values ranged from 0.05 to 0.84 with an overall mean of 0.64. Un-weighted neighbour joining clustering put 23 genotypes in two main clusters, which were further subdivided into 5 and 6 sub-clusters, respectively. We obtained 56 rare and 26 unique alleles in specific inbred lines, which can be used for identification of these lines. The present study has revealed considerable diversity among inbred lines differing for resistance against PFSR and pink borer; and provided ample scope for selection of parents for utilization in heterosis breeding