Comparison of the observed with the simulated distributions of the parental genome contribution in two marker-assisted backcross programs in rice

Computer simulations are useful tools to optimize marker-assisted breeding programs. The objective of our study was to investigate the closeness of computer simulations of the recurrent parent genome recovery with experimental data obtained in two marker-assisted backcrossing programs in rice (Orzya sativa L.). We simulated the breeding programs as they were practically carried out. In the simulations we estimated the frequency distributions of the recurrent parent genome proportion in the backcross populations. The simulated distributions were in good agreement with those obtained practically. The simulation results were also observed to be robust with respect to the choice of the mapping function and the accuracy of the linkage map. We conclude that computer simulations are a useful tool for pre-experiment estimation of selection response in marker-assisted backcrossing. Vanessa Prigge and Hans Peter Maurer contributed equally to this work.     

Association mapping in multiple segregating populations of sugar beet (<Emphasis Type="Italic">Beta vulgaris</Emphasis> L.)

Association mapping in multiple segregating populations (AMMSP) combines high power to detect QTL in genome-wide approaches of linkage mapping with high mapping resolution of association mapping. The main objectives of this study were to (1) examine the applicability of AMMSP in a plant breeding context based on segregating populations of various size of sugar beet (Beta vulgaris L.), (2) compare different biometric approaches for AMMSP, and (3) detect markers with significant main effect across locations for nine traits in sugar beet. We used 768 F _n (n = 2, 3, 4) sugar beet genotypes which were randomly derived from 19 crosses among diploid elite sugar beet clones. For all nine traits, the genotypic and genotype × location interaction variances were highly significant (P < 0.01). Using a one-step AMMSP approach, the total number of significant (P < 0.05) marker-phenotype associations was 44. The identification of genome regions associated with the traits under consideration indicated that not only segregating populations derived from crosses of parental genotypes in a systematic manner could be used for AMMSP but also populations routinely derived in plant breeding programs from multiple, related crosses. Furthermore, our results suggest that data sets, whose size does not permit analysis by the one-step AMMSP approach, might be analyzed using the two-step approach based on adjusted entry means for each location without losing too much power for detection of marker-phenotype associations.     

Re-evaluation of the prospects of marker-assisted selection for improving insect resistance against Diatraea spp. in tropical maize by cross validation and independent validation

Cross validation (CV) and validation with an independent sample (IV) are new biometric approaches in QTL analysis to obtain unbiased estimates of QTL effects and the proportion of the genetic variance explained by the detected marker-QTL association (p). Our objective with these methods was to obtain a realistic picture on the prospects of marker-assisted selection (MAS) for improving the resistance of maize against the tropical stem borer species Diatraea grandiosella (SWCB) and Diatraea saccharalis (SCB). Published QTL mapping studies on leaf-damage ratings (LDR) with populations of F_2:3 lines and recombinant inbred lines (RIL) from crosses CML131×CML67 and Ki3× CML139 of tropical maize inbreds were re-analyzed with CV and IV. With CV, the reduction in p for LDR compared to p obtained with the whole data set varied between 41.0 and 79.6% in the populations of F_2:3 lines and between 30.1 and 65.2% in the two populations of RIL. Estimates of p for SCB LDR were similar for CV and IV. For SWCB LDR, p estimates obtained with IV were larger than those obtained with CV in CML131× CML67. The reverse was observed for Ki3×CML139. Under the assumption of identical selection intensities, and based on the re-estimates of p, MAS using only molecular marker information is less-efficient than conventional phenotypic selection (CPS). MAS combining marker and phenotypic data increases the relative efficiency by only 4% in comparison to CPS. In conclusion, MAS for improving SWCB and SCB LDR seems not-promising unless additional QTLs with proven large effects are available or the costs of marker assays are considerably reduced. Received: 7 December 2000 / Accepted: 5 February 2001     

Variation of DNA fingerprints among accessions within maize inbred lines and implications for identification of essentially derived varieties.

Genetic distances (GDs) based on molecular markers are important parameters for identifying essentially derived varieties (EDVs). In this context information about the variability of molecular markers within maize inbred lines is essential. Our objectives were to (1) determine the variation in the size of simple sequence repeat (SSR) fragments among different accessions of maize inbreds and doubled haploid (DH) lines, (2) attribute the observed variation to genetic and marker system-specific sources, and (3) investigate the effect of SSR fragment size differences within maize lines on the GD between maize lines and their consequences for the identification of essentially derived varieties. Two to five accessions from nine inbred lines and five DH lines were taken from different sources or drawn as independent samples from the same seed lot. Each accession was genotyped with 100 SSR markers that evenly covered the whole maize genome. In total, 437 SSR fragments were identified, with a mean of 4.4 alleles per locus. The average polymorphic information content (PIC) was 0.58. GD estimates between two accessions of the same genotype ranged from 0.00 to 0.12 with an average of 0.029 for inbred lines and 0.001 for DH lines. An average of 11.1 SSRs was polymorphic between accessions of the same inbred line due to non-amplification (8.1 SSRs), heterogeneity (4.0 SSRs) or unknown alleles (2.6 SSRs). In contrast to lab errors, heterogeneity contributed considerably to the observed variation for GD. In order to decrease the probability to be suited for infringing an EDV threshold by chance, we recommend to increase the level of homogeneity of inbred lines before applying for plant variety protection.     

Metabolic robustness in young roots underpins a predictive model of maize hybrid performance in the field

Heterosis has been extensively exploited for yield gain in maize (Zea mays L.). Here we conducted a comparative metabolomics‐based analysis of young roots from in vitro germinating seedlings and from leaves of field‐grown plants in a panel of inbred lines from the Dent and Flint heterotic patterns as well as selected F₁ hybrids. We found that metabolite levels in hybrids were more robust than in inbred lines. Using state‐of‐the‐art modeling techniques, the most robust metabolites from roots and leaves explained up to 37 and 44% of the variance in the biomass from plants grown in two distinct field trials. In addition, a correlation‐based analysis highlighted the trade‐off between defense‐related metabolites and hybrid performance. Therefore, our findings demonstrated the potential of metabolic profiles from young maize roots grown under tightly controlled conditions to predict hybrid performance in multiple field trials, thus bridging the greenhouse–field gap.     

Genotyping-by-sequencing highlights original diversity patterns within a European collection of 1191 maize flint lines,as compared to the maize USDA genebank

Key message

Genotyping by sequencing is suitable for analysis of global diversity in maize. We showed the distinctiveness of flint maize inbred lines of interest to enrich the diversity of breeding programs.

Abstract

Genotyping-by-sequencing (GBS) is a highly cost-effective procedure that permits the analysis of large collections of inbred lines. We used it to characterize diversity in 1191 maize flint inbred lines from the INRA collection, the European Cornfed association panel, and lines recently derived from landraces. We analyzed the properties of GBS data obtained with different imputation methods, through comparison with a 50 K SNP array. We identified seven ancestral groups within the Flint collection (dent, Northern flint, Italy, Pyrenees–Galicia, Argentina, Lacaune, Popcorn) in agreement with breeding knowledge. Analysis highlighted many crosses between different origins and the improvement of flint germplasm with dent germplasm. We performed association studies on different agronomic traits, revealing SNPs associated with cob color, kernel color, and male flowering time variation. We compared the diversity of both our collection and the USDA collection which has been previously analyzed by GBS. The population structure of the 4001 inbred lines confirmed the influence of the historical inbred lines (B73, A632, Oh43, Mo17, W182E, PH207, and Wf9) within the dent group. It showed distinctly different tropical and popcorn groups, a sweet-Northern flint group and a flint group sub-structured in Italian and European flint (Pyrenees–Galicia and Lacaune) groups. Interestingly, we identified several selective sweeps between dent, flint, and tropical inbred lines that co-localized with SNPs associated with flowering time variation. The joint analysis of collections by GBS offers opportunities for a global diversity analysis of maize inbred lines.

     

Precision of recombination frequency estimates after random intermating with finite population sizes

Random intermating of F2 populations has been suggested for obtaining precise estimates of recombination frequencies between tightly linked loci. In a simulation study, sampling effects due to small population sizes in the intermating generations were found to abolish the advantages of random intermating that were reported in previous theoretical studies considering an infinite population size. We propose a mating scheme for intermating with planned crosses that yields more precise estimates than those under random intermating.     

Germination of <i>Eryngium regnellii</i>: a major species for ecological restoration of plant-pollinator interactions in the Southern Pampas (Buenos Aires,Argentina)

Eryngium regnellii Malme belongs to the largest genera in the Apiaceae family, with 250 species worldwide and 65 represented in South America. It is a herbaceous species typical of hill plant communities, which, along with remnant grassland patches, are the most relevant natural habitats for the maintenance of diversity in the Southern Pampas. Eryngium regnellii is key to the maintenance of pollination mutualisms, being a generalist (displaying a diverse assemblage of pollinators) and ubiquitous species (present in all studied sierras). However, fragmentation of the Pampean landscape due to agricultural intensification has led to the loss of natural environments. Therefore, the reintroduction of E. regnellii in strategic places would facilitate the occurrence of wild pollinators, while favoring pollination services in the agroecosystem. The germination requirements of E. regnellii were studied because a better knowledge of the reproductive biology of this species would provide information relevant to its reproduction and reintroduction into degraded areas. Germination percentages and mean time to germination were evaluated, using one control and two pre-germination treatments: chemical scarification with sulfuric acid, and mechanical scarification with sand paper. Chemical scarified seeds did not germinate. Mechanically scarified and control seed groups showed no significant differences either in germination percentages (49% and 59% respectively) or in mean germination time (13 and 14 days, respectively). Results indicate that E. regnellii shows no physical dormancy, and does not require specific pre-germination treatments for germination under the studied laboratory conditions. The high germination capacity of E. regnellii, along with its ecological attributes, make it a potential species for restoring plant-pollinator interactions in the fragmented landscapes of the Southern Pampas.