Use of SSRs for establishing heterotic groups in subtropical maize

Heterotic groups and patterns are of fundamental importance in hybrid breeding. The objectives of our research were to: (1) investigate the relationship of simple sequence repeats (SSR) based genetic distances between populations and panmictic midparent heterosis (PMPH) in a broad range of CIMMYT maize germplasm, (2) evaluate the usefulness of SSR markers for defining heterotic groups and patterns in subtropical germplasm, and (3) examine applications of SSR markers for broadening heterotic groups by systematic introgression of other germplasm. Published data of two diallels and one factorial evaluated for grain yield were re-analyzed to calculate the PMPH in population hybrids. Additionally, 20 pools and populations widely used in CIMMYT's breeding program were assayed with 83 SSR markers covering the entire maize genome. Correlations of squared modified Roger's distance (MRD²) and PMPH were mostly positive and significant, but adaption problems caused deviations in some cases. For intermediate- and early-maturity subtropical germplasm, two heterotic groups could be suggested consisting of a flint and dent composite. We concluded that the relationships between the populations obtained by SSR analyses are in excellent agreement with pedigree information. SSR markers are a valuable complementation to field trials for identifying heterotic groups and can be used to introgress exotic germplasm systematically.Communicated by F. Salamini     

Broadening the genetic base of European maize heterotic pools with US Cornbelt germplasm using field and molecular marker data

Maize (Zea mays L.) breeders are concerned about the narrowing of the genetic base of elite germplasm. To reverse this trend, elite germplasm from other geographic regions can be introgressed, but due to lack of adaptation it is difficult to assess their breeding potential in the targeted environment. The objectives of this study were to (1) investigate the relationship between European and US maize germplasm, (2) examine the suitability of different mega-environments and measures of performance to assess the breeding potential of exotics, and (3) study the relationship of genetic distance with mid-parent heterosis (MPH). Eight European inbreds from the Dent and Flint heterotic groups, 11 US inbreds belonging to Stiff Stalk (SS), non-Stiff Stalk (NSS), and CIMMYT Pool 41, and their 88 factorial crosses in F₁ and F₂ generations were evaluated for grain yield and dry matter concentration. The experiments were conducted in three mega-environments: Central Europe (target mega-environment), US Cornbelt (mega-environment where donor lines were developed), and Southeast Europe (an intermediate mega-environment). The inbreds were also fingerprinted with 266 SSR markers. Suitable criteria to identify promising exotic germplasm were F₁ hybrid performance in the targeted mega-environment and F₁ and parental performance in the intermediate mega-environment. Marker-based genetic distances reflected relatedness among the inbreds, but showed no association with MPH. Based on genetic distance, MPH, and F₁ performance, we suggest to introgress SS germplasm into European Dents and NSS into European Flints, in order to exploit the specific adaptation of European flint germplasm and the excellent combining ability of US germplasm in European maize breeding programs.     

Prediction of single-cross hybrid performance in maize using haplotype blocks associated with QTL for grain yield

Marker-based prediction of hybrid performance facilitates the identification of untested single-cross hybrids with superior yield performance. Our objectives were to (1) determine the haplotype block structure of experimental germplasm from a hybrid maize breeding program, (2) develop models for hybrid performance prediction based on haplotype blocks, and (3) compare hybrid performance prediction based on haplotype blocks with other approaches, based on single AFLP markers or general combining ability (GCA), under a validation scenario relevant for practical breeding. In total, 270 hybrids were evaluated for grain yield in four Dent × Flint factorial mating experiments. Their parental inbred lines were genotyped with 20 AFLP primer–enzyme combinations. Adjacent marker loci were combined into haplotype blocks. Hybrid performance was predicted on basis of single marker loci and haplotype blocks. Prediction based on variable haplotype block length resulted in an improved prediction of hybrid performance compared with the use of single AFLP markers. Estimates of prediction efficiency (R ² ) ranged from 0.305 to 0.889 for marker-based prediction and from 0.465 to 0.898 for GCA-based prediction. For inter-group hybrids with predominance of general over specific combining ability, the hybrid prediction from GCA effects was efficient in identifying promising hybrids. Considering the advantage of haplotype block approaches over single marker approaches for the prediction of inter-group hybrids, we see a high potential to substantially improve the efficiency of hybrid breeding programs. Tobias A. Schrag and Hans Peter Maurer contributed equally to this work.     

Determination of heterotic groups for tropical Indica hybrid rice germplasm

Key message

Two heterotic groups and four heterotic patterns were identified for IRRI hybrid rice germplasm to develop hybrid rice in the tropics based on SSR molecular data and field trials.

Abstract

Information on heterotic groups and patterns is a fundamental prerequisite for hybrid crop breeding; however, no such clear information is available for tropical hybrid rice breeding after more than 30 years of hybrid rice commercialization. Based on a study of genetic diversity using molecular markers, 18 parents representing hybrid rice populations historically developed at the International Rice Research Institute (IRRI) were selected to form diallel crosses of hybrids and were evaluated in tropical environments. Yield, yield heterosis and combining ability were investigated with the main objectives of (1) evaluating the magnitude of yield heterosis among marker-based parental groups, (2) examining the consistency between marker-based group and heterotic performance of hybrids, and (3) identifying foundational hybrid parents in discrete germplasm pools to provide a reference for tropical indica hybrid rice breeding. Significant differences in yield, yield heterosis and combining ability were detected among parents and among hybrids. On average, the hybrids yielded 14.8 % higher than the parents. Results revealed that inter-group hybrids yielded higher, with higher yield heterosis than intra-group hybrids. Four heterotic patterns within two heterotic groups based on current IRRI B- and R-line germplasm were identified. Parents in two marker-based groups were identified with limited breeding value among current IRRI hybrid rice germplasm because of their lowest contribution to heterotic hybrids. Heterotic hybrids are significantly correlated with high-yielding parents. The efficiency of breeding heterotic hybrids could be enhanced using selected parents within identified marker-based heterotic groups. This information is useful for exploiting those widely distributed IRRI hybrid rice parents.     

Hybrid performance in taro (<Emphasis Type="Italic">Colocasia esculenta</Emphasis>) in relation to genetic dissimilarity of parents

Taro (Colocasia esculenta) breeding, as other root crop breeding, is based on the production and evaluation of large numbers of hybrids. The selection of parents is based on their phenotypic value in the absence of information concerning general combining ability (GCA), specific combining ability (SCA), or genetic distances between varieties. By combining data from heritability trials and from genetic diversity studies conducted with AFLP and SSR markers, we aimed at studying the relationship between hybrid vigour and genetic dissimilarity between parents. The traits studied included number of suckers, corm weight, corm dimensions, and dry matter content. Correlation coefficients between hybrid gain and dissimilarity values were calculated. The prediction of hybrid performance based on the mid-parent value was compared to the prediction based on a modified expression that takes into account the genetic relationships between parents. Correlations were all but one positive but not statistically significant for all traits, with the exception of the number of suckers, when using SSR markers for dissimilarity calculations. Accordingly, the genetic dissimilarities in the prediction of hybrid performances did not increase the correlation between predicted and observed hybrid vigour values. However, large differences were observed among the residual means from the regression between predicted and observed values when using AFLP or SSR markers, mainly due to the much higher polymorphism revealed by the latter. Models need to be further adapted to the type of molecular marker used, since their ability to reveal different rates of polymorphism will have a direct incidence on the calculation of genetic dissimilarities between genotypes. Nevertheless, since SSR markers are more polymorphic and more informative than AFLP markers, they should be preferentially used for these studies. Low genetic dissimilarity of parents yielded weak heterosis effects and future studies need to be conducted by using a broader genetic base. This is the first study assessing the relationship of hybrid vigour with the genetic distances between parents, conducted on a tropical root crop.     

The strategy and potential utilization of temperate germplasm for tropical germplasm improvement: a case study of maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.)

The organization of maize (Zea mays L.) germplasm into genetically divergent heterotic groups is the foundation of a successful hybrid maize breeding program. In this study, 94 CIMMYT maize lines (CMLs) and 54 United States germplasm enhancement of maize (GEM) lines were assembled and characterized using 1,266 single nucleotide polymorphisms (SNPs) with high quality. Based on principal component analysis (PCA), the GEM lines and CMLs were clearly separated. In the GEM lines, there were two groups classified by PCA corresponding to the heterotic groups “stiff stalk” and “non-stiff stalk”. CMLs did not form obvious subgroups by PCA. The allelic frequency of each SNP differed in GEM lines and CMLs. In total, 3.6% alleles (46/1,266) of CMLs are absent in GEM lines and 4.4% alleles (56/1,266) of GEM lines are absent in CMLs. The performance of F1 plants (n = 654) produced by crossing between different groups based on pedigree information was evaluated at the breeding nurseries of two CIMMYT stations. Genomic estimated phenotypic values of plant height and days to anthesis for a testing set of 45 F1 crosses were predicted based on the training data of 600 F1 crosses using a best linear unbiased prediction method. The prediction accuracy benefitted from the adoption of the markers associated with quantitative trait loci for both traits; however, it does not necessarily increase with an increase in marker density. It is suggested that genomic selection combined with association analysis could improve prediction efficiency and reduce cost. For hybrid maize breeding in the tropics, incorporating GEM lines which have unique alleles and clear heterotic patterns into tropically adapted lines could be beneficial for enhancing heterosis in grain yields.     

Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms

Characterization of genetic diversity is of great value to assist breeders in parental line selection and breeding system design. We screened 770 maize inbred lines with 1,034 single nucleotide polymorphism (SNP) markers and identified 449 high-quality markers with no germplasm-specific biasing effects. Pairwise comparisons across three distinct sets of germplasm, CIMMYT (394), China (282), and Brazil (94), showed that the elite lines from these diverse breeding pools have been developed with only limited utilization of genetic diversity existing in the center of origin. Temperate and tropical/subtropical germplasm clearly clustered into two separate groups. The temperate germplasm could be further divided into six groups consistent with known heterotic patterns. The greatest genetic divergence was observed between temperate and tropical/subtropical lines, followed by the divergence between yellow and white kernel lines, whereas the least divergence was observed between dent and flint lines. Long-term selection for hybrid performance has contributed to significant allele differentiation between heterotic groups at 20% of the SNP loci. There appeared to be substantial levels of genetic variation between different breeding pools as revealed by missing and unique alleles. Two SNPs developed from the same candidate gene were associated with the divergence between two opposite Chinese heterotic groups. Associated allele frequency change at two SNPs and their allele missing in Brazilian germplasm indicated a linkage disequilibrium block of 142 kb. These results confirm the power of SNP markers for diversity analysis and provide a feasible approach to unique allele discovery and use in maize breeding programs.     

Heterotic patterns in rapeseed (<Emphasis Type="Italic">Brassica napus</Emphasis> L.): I. Crosses between spring and Chinese semi-winter lines

Chinese semi-winter rapeseed is genetically diverse from Canadian and European spring rapeseed. This study was conducted to evaluate the potential of semi-winter rapeseed for spring rapeseed hybrid breeding, to assess the genetic effects involved, and to estimate the correlation of parental genetic distance (GD) with hybrid performance, heterosis, general combining ability (GCA) and specific combining ability (SCA) in crosses between spring and semi-winter rapeseed lines. Four spring male sterile lines from Germany and Canada as testers were crossed with 13 Chinese semi-winter rapeseed lines to develop 52 hybrids, which were evaluated together with their parents and commercial hybrids for seed yield and oil content in three sets of field trials with 8 environments in Canada and Europe. The Chinese parental lines were not adapted to local environmental conditions as demonstrated by poor seed yields per se. However, the hybrids between the Chinese parents and the adapted spring rapeseed lines exhibited high heterosis for seed yield. The average mid-parent heterosis was 15% and ca. 50% of the hybrids were superior to the respective hybrid control across three sets of field trials. Additive gene effects mainly contributed to hybrid performance since the mean squares of GCA were higher as compared to SCA. The correlation between parental GD and hybrid performance and heterosis was found to be low whereas the correlation between GCA_{(f + m)} and hybrid performance was high and significant in each set of field trials, with an average of r = 0.87 for seed yield and r = 0.89 for oil content, indicating that hybrid performance can be predicted by GCA_{(f + m)}. These results demonstrate that Chinese semi-winter rapeseed germplasm has a great potential to increase seed yield in spring rapeseed hybrid breeding programs in Canada and Europe.     

DNA based iPBS-retrotransposon markers for investigating the population structure of pea (Pisum sativum) germplasm from Turkey

Retrotransposons have been highly studied in monocots; however retrotransposon diversity in dicot crops has not been well documented. Our objective was to assess the diversity harbored by field pea landraces using retrotranposon markers. In this research, molecular characterization of 104 landraces and 34 field pea breeding lines was assessed using newly developed iPBS-retrotransposon markers. The 12 iPBS-retrotransposon primers generated a total 106 scorable bands, and 81 of these were found to be polymorphic (76.4%), with an average of 6.75 polymorphic fragments per primer. Polymorphism information content (PIC) ranged from 0.33 to 0.84 with an average of 0.61. It was evident that field pea landraces from the same geographical region were often placed in different groups in the neighbor joining analysis, indicating that grouping based on genetic parameters was not closely related to the geographical origin. The population structure was determined by using STRUCTURE software, and three populations at K = 3 and five populations at K = 5 were identified among landraces. The plentiful diversity present in Turkish field pea landraces could be used as genetic resource in designing breeding program, and may also contribute to worldwide pea breeding programs. Our data also suggested a role of iPBS-retrotransposons as ‘a universal marker’ for molecular characterization of pea germplasm.     

Molecular marker-based prediction of hybrid performance in maize using unbalanced data from multiple experiments with factorial crosses

In hybrid breeding, the prediction of hybrid performance (HP) is extremely important as it is difficult to evaluate inbred lines in numerous cross combinations. Recent developments such as doubled haploid production and molecular marker technologies have enhanced the prospects of marker-based HP prediction to accelerate the breeding process. Our objectives were to (1) predict HP using a combined analysis of hybrids and parental lines from a breeding program, (2) evaluate the use of molecular markers in addition to phenotypic and pedigree data, (3) evaluate the combination of line per se data with marker-based estimates, (4) study the effect of the number of tested parents, and (5) assess the advantage of haplotype blocks. An unbalanced dataset of 400 hybrids from 9 factorial crosses tested in different experiments and data of 79 inbred parents were subjected to combined analyses with a mixed linear model. Marker data of the inbreds were obtained with 20 AFLP primer–enzyme combinations. Cross-validation was used to assess the performance prediction of hybrids of which no or only one parental line was testcross evaluated. For HP prediction, the highest proportion of explained variance (R ²), 46% for grain yield (GY) and 70% for grain dry matter content (GDMC), was obtained from line per se best linear unbiased prediction (BLUP) estimates plus marker effects associated with mid-parent heterosis (TEAM-LM). Our study demonstrated that HP was efficiently predicted using molecular markers even for GY when testcross data of both parents are not available. This can help in improving greatly the efficiency of commercial hybrid breeding programs.     

SSR heterogenic patterns of parents for marking and predicting heterosis in rice breeding

The most important concerns of hybrid rice breeders are selection of donors to improve parental lines and prediction of hybrid performance. In this study, SSR molecular marker technology and a half-diallel method were used to address these related hybrid production issues. The results show that genetic diversity among the parental lines is certainly related to heterosis. The heterozygosity of each parental pair is significantly associated with the general combining ability, not with the specific combining ability. However, neither genetic diversity nor heterozygosity is a good indicator for predicting heterosis. From these results, it is suggested that donors for improving parents of hybrids be selected from the improved inbred lines by conventional breeding programs. In this investigation, we also discovered that four favorable alleles and six favorable heterogenic patterns on the parental lines significantly contribute to the heterosis of their hybrids in grain yield, whereas six unfavorable alleles and six unfavorable heterogenic patterns significantly reduce heterosis. These noticeable findings could be, in practice, useful for hybrid rice breeding programs with SSR marker-assisted selection. It is suggested that the optimal combinations with the superior grain yield could be bred out by assembling those favorable alleles into their parental lines and by removing the unfavorable alleles from the parental lines. This study also indicates that there is still a great heterosis potential to be exploited in indica/indica hybrids by the same strategy. In indica/japonica hybrid breeding programs, it may also be important to remove unfavorable alleles rather than broaden genetic diversity or heterozygosity of the parents.     

Hybrid wheat: quantitative genetic parameters and consequences for the design of breeding programs

Key message

Commercial heterosis for grain yield is present in hybrid wheat but long-term competiveness of hybrid versus line breeding depends on the development of heterotic groups to improve hybrid prediction.

Abstract

Detailed knowledge of the amount of heterosis and quantitative genetic parameters are of paramount importance to assess the potential of hybrid breeding. Our objectives were to (1) examine the extent of midparent, better-parent and commercial heterosis in a vast population of 1,604 wheat (Triticum aestivum L.) hybrids and their parental elite inbred lines and (2) discuss the consequences of relevant quantitative parameters for the design of hybrid wheat breeding programs. Fifteen male lines were crossed in a factorial mating design with 120 female lines, resulting in 1,604 of the 1,800 potential single-cross hybrid combinations. The hybrids, their parents, and ten commercial wheat varieties were evaluated in multi-location field experiments for grain yield, plant height, heading time and susceptibility to frost, lodging, septoria tritici blotch, yellow rust, leaf rust, and powdery mildew at up to five locations. We observed that hybrids were superior to the mean of their parents for grain yield (10.7 %) and susceptibility to frost (?7.2 %), leaf rust (?8.4 %) and septoria tritici blotch (?9.3 %). Moreover, 69 hybrids significantly (P < 0.05) outyielded the best commercial inbred line variety underlining the potential of hybrid wheat breeding. The estimated quantitative genetic parameters suggest that the establishment of reciprocal recurrent selection programs is pivotal for a successful long-term hybrid wheat breeding.     

杂交稻特殊配合力与杂种优势、亲本间遗传距离的相 关性

杂交水稻育种的实质是配合力育种, 筛选高特殊配合力的杂交水稻组合才能选育出在生产上有实用价值的强优势组合。文章利用SSR标记检测了9个三系杂交稻亲本(5个不育系和4个恢复系)之间的遗传距离, 结合20个杂交稻组合(5×4 NCII)的产量表现, 分析了杂交水稻特殊配合力(Special combining ability, SCA)效应与产量杂种优势、亲本间遗传距离的相关性。结果表明, 特殊配合力效应与对照优势(相关系数r₁=0.5609)、平均优势(相关系数_r2=0.541)之间均呈显著正相关, 而与亲本遗传距离之间相关不显著, 相关系数(r=0.2143)较小。说明本研究所配组合的特殊配合力效应能充分反映杂种优势, 选用的杂交亲本能组配出强优势组合; 而杂交亲本遗传距离的大小并不能反映特殊配合力效应, 分子标记遗传距离与特殊配合力的相关性还有待于进一步的探讨。     

Romanian Maize (Zea mays) Inbred Lines as a Source of Genetic Diversity in SE Europe,and Their Potential in Future Breeding Efforts

Maize has always been under constant human selection ever since it had been domesticated. Intensive breeding programs that resulted in the massive use of hybrids nowadays have started in the 60s. That brought significant yield increases but reduced the genetic diversity at the same time. Consequently, breeders and researchers alike turned their attention to national germplasm collections established decades ago in many countries, as they may hold allelic variations that could prove useful for future improvements. These collections are mainly composed of inbred lines originating from well-adapted local open pollinated varieties. However, there is an overall lack of data in the literature about the genetic diversity of maize in SE Europe, and its potential for future breeding efforts. There are no data, whatsoever, on the nutritional quality of the grain, primarily dictated by the zein proteins. We therefore sought to use the Romanian maize germplasm as an entry point in understanding the molecular make-up of maize in this part of Europe. By using 80 SSR markers, evenly spread throughout the genome, on 82 inbred lines from various parts of the country, we were able to decipher population structure and the existing relationships between those and the eight international standards used, including the reference sequenced genome B73. Corroborating molecular data with a standardized morphological, physiological, and biochemical characterization of all 90 inbred lines, this is the first comprehensive such study on the existing SE European maize germplasm. The inbred lines we present here are an important addition to the ever-shrinking gene pool that the breeding programs are faced-with, because of the allelic richness they hold. They may serve as parental lines in crosses that will lead to new hybrids, characterized by a high level of heterosis, nationwide and beyond, due to their existing relationship with the international germplasm.     

Grouping of tropical mid-altitude maize inbred lines on the basis of yield data and molecular markers

The classification of maize inbred lines into heterotic groups is an important undertaking in hybrid breeding. The objectives of our research were to: (1) separate selected tropical mid-altitude maize inbred lines into heterotic groups based on grain yield data; (2) assess the genetic relationships among these inbred lines using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers; (3) examine the consistency between yield-based and marker-based groupings of the inbred lines. Thirty-eight tropical mid-altitude maize inbred lines were crossed to two inbred line testers representing the flint and dent heterotic pattern, respectively. The resulting testcrosses were evaluated in a trial at three locations for 2 years. Significant general combining ability (GCA) and specific combining ability (SCA) effects for grain yield were detected among the inbred lines. The tester inbred lines classified 23 of the 38 tested inbred lines into two heterotic groups based on SCA effects and testcross mean grain yields. This grouping was not related to endosperm type of the inbred lines. The outstanding performance of testcrosses of the remaining 15 inbred lines indicates the presence of significant genetic diversity that may allow the assignment of the lines into more than two heterotic groups. Diversity analysis of the 40 maize inbred lines using AFLP and SSR markers found high levels of genetic diversity among these lines and subdivided them into two main groups with subdivision into sub-groups consistent with breeding history, origin and parentage of the lines. However, heterotic groups formed using yield-based combining ability were different from the groups established on the basis of molecular markers. Considering the diversity of the genetic backgrounds of the mid-altitude inbred lines, the marker-based grouping may serve as the basis to design and carry out combining ability studies in the field to establish clearly defined heterotic groups with a greater genetic similarity within groups.Communicated by H.H. Geiger     

General and specific combining abilities in a maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) test-cross hybrid panel: relative importance of population structure and genetic divergence between parents

Key message

General and specific combining abilities of maize hybrids between 288 inbred lines and three tester lines were highly related to population structure and genetic distance inferred from SNP data.

Abstract

Many studies have attempted to provide reliable and quick methods to identify promising parental lines and combinations in hybrid breeding programs. Since the 1950s, maize germplasm has been organized into heterotic groups to facilitate the exploitation of heterosis. Molecular markers have proven efficient tools to address the organization of genetic diversity and the relationship between lines or populations. The aim of the present work was to investigate to what extent marker-based evaluations of population structure and genetic distance may account for general (GCA) and specific (SCA) combining ability components in a population composed of 800 inter and intra-heterotic group hybrids obtained by crossing 288 inbred lines and three testers. Our results illustrate a strong effect of groups identified by population structure analysis on both GCA and SCA components. Including genetic distance between parental lines of hybrids in the model leads to a significant decrease of SCA variance component and an increase in GCA variance component for all the traits. The latter suggests that this approach can be efficient to better estimate the potential combining ability of inbred lines when crossed with unrelated lines, and limits the consequences of tester choice. Significant residual GCA and SCA variance components of models taking into account structure and/or genetic distance highlight the variation available for breeding programs within structure groups.

     

Genetic diversity of African maize inbred lines revealed by SSR markers

Knowledge of genetic diversity (GD) and relationships among maize inbred lines is indispensable in a breeding program. Our objectives were to (1) investigate the level of genetic diversity among maize inbred lines and (2) assess their genetic structures by applying simple sequence repeat (SSR) markers. Fifty-six highland and mid-altitude maize inbred lines obtained from CIMMYT programs in Ethiopia and Zimbabwe were genotyped using 27 SSR loci. All of the genotypes studied could unequivocally be distinguished with the combination of the SSRs used. In total, 104 SSR alleles were identified, with a mean of 3.85 alleles per locus. The average polymorphism information content (PIC) was 0.58. GD expressed as Euclidean distance, varied from 0.28 to 0.73 with an average of 0.59. Cluster analysis using unweighted pair group method with arithmetic average (UPGMA) suggested five groups among the inbred lines. Most of the inbred lines adapted to the highlands and the mid-altitudes were positioned in different clusters with a few discrepancies. The pattern of groupings of the inbred lines was mostly consistent with available pedigree information. The variability detected using SSR markers could potentially contribute towards effective utilization of the inbred lines for the exploitation of heterosis and formation of genetically diverse source populations in Ethiopian maize improvement programs.