Genetic Diversity for Restriction Fragment Length Polymorphisms: Relation to Estimated Genetic Effects in Maize Inbreds

Restriction fragment length polymorphisms (RFLPs) have been proposed for investigating relationships among inbred lines and predicting heterosis and performance of single-cross hybrids in maize (Zea mays L.). Such use was evaluated in 20 maize inbreds classified as first-cycle, second-cycle, good, and poor lines, and in diallel crosses within types. Eight generations (parents, F1, F2, F3, backcrosses, and backcrosses selfed) from 67 crosses were evaluated for grain yield in five Iowa environments. Genetic effects were estimated from generation means by ordinary diallel analyses and the Eberhart-Gardner genetic model. Poor inbreds showed significantly greater average heterosis than did good lines. Estimates of additive ✕ additive epistatic effects were negative and highly significant in all except first-cycle lines. Using two restriction enzymes and 82 genomic) DNA probes distributed throughout the maize genome, all but one probe revealed polymorphisms with at least one enzyme (~4.5 variants per RFLP locus). Genetic distances between lines within types were estimated as Rogers\u27 distances (RD). Within diallel sets, RD values were partitioned into general (GRD)and specific (SRD). All four types of lines showed similar means and substantial variation for RD; GRD explained ~40% of the variation among RD values. Cluster analyses revealed associations among lines generally consistent with expectations based on known pedigrees. Correlations of RD and SRD with F1 yield heterosis, specific heterosis, and specific combining ability were positive but small (r = ≤ 0.50) when combined for all crosses. Results indicated that RFLPs can be used to investigate pedigree relationships among maize inbreds, but also suggest that RFLP-based genetic distance measures are of limited use in predicting heterotic performance of single crosses between unrelated lines

Dissecting grain yield pathways and their interactions with grain dry matter content by a two-step correlation approach with maize seedling transcriptome

<p>Abstract</p> <p>Background</p> <p>The importance of maize for human and animal nutrition, but also as a source for bio-energy is rapidly increasing. Maize yield is a quantitative trait controlled by many genes with small effects, spread throughout the genome. The precise location of the genes and the identity of the gene networks underlying maize grain yield is unknown. The objective of our study was to contribute to the knowledge of these genes and gene networks by transcription profiling with microarrays.</p> <p>Results</p> <p>We assessed the grain yield and grain dry matter content (an indicator for early maturity) of 98 maize hybrids in multi-environment field trials. The gene expression in seedlings of the parental inbred lines, which have four different genetic backgrounds, was assessed with genome-scale oligonucleotide arrays. We identified genes associated with grain yield and grain dry matter content using a newly developed two-step correlation approach and found overlapping gene networks for both traits. The underlying metabolic pathways and biological processes were elucidated. Genes involved in sucrose degradation and glycolysis, as well as genes involved in cell expansion and endocycle were found to be associated with grain yield.</p> <p>Conclusions</p> <p>Our results indicate that the capability of providing energy and substrates, as well as expanding the cell at the seedling stage, highly influences the grain yield of hybrids. Knowledge of these genes underlying grain yield in maize can contribute to the development of new high yielding varieties.</p

Genetic diversity among progenitors and elite lines from the Iowa Stiff Stalk Synthetic (BSSS) maize population: comparison of allozyme and RFLP data

Data for restriction fragment length polymorphisms (RFLPs) of 144 clone-enzyme combinations and for 22 allozyme loci from 21 U.S. Corn Belt maize (Zea mays L.) inbreds were analyzed. The genetic materials included 14 progenitors of the Iowa Stiff Stalk Synthetic (BSSS) maize population, both parents of one missing BSSS progenitor, four elite inbreds derived from BSSS, and inbred Mo17. Objectives were to characterize the genetic variation among these 21 inbreds for both allozymes and RFLPs, to compare the results from both types of molecular markers, and to estimate the proportion of unique alleles in the BSSS progenitors. Genetic diversity among the 21 inbreds was substantially greater for RFLPs than for allozymes, but the percentages of unique RFLP variants (27%) and unique allozyme alleles (25%) in the BSSS progenitors were similar. Genetic distances between inbreds, estimated as Rogers\u27 distance (RD), were, on average, twice as large for RFLP (0.51) as for allozyme data (0.24). RDs obtained from allozyme and RFLP data for individual line combinations were only poorly correlated (r = 0.23); possible reasons for discrepancies are discussed. Principal component analysis of RFLP data, in contrast to allozyme data, resulted in separate groupings of the ten BSSS progenitors derived from the ‘Reid Yellow Dent’ population, the four BSSS elite lines, and Mo17. The remaining six BSSS progenitors were genetically rather diverse and contributed a large number of rare alleles to BSSS. The results of this study corroborate the fact that RFLPs are superior to allozymes for characterizing the genetic diversity of maize breeding materials, because of (1) the almost unlimited number of markers available and (2) the greater amount of polymorphisms found. In particular, RFLPs allow related lines and inbreds with common genetic background to be identified, but a large number of probe-enzyme combinations is needed to estimate genetic distances with the precision required

Rachis brittleness in a hybrid–parent barley (Hordeum vulgare) breeding germplasm with different combinations at the non‐brittle rachis genes

Two dominant, closely linked and complementary genes, Btr1 and Btr2, control rachis brittleness in barley. Recessive mutations in any of these genes turn the fragile rachis (brittle) into a tough rachis phenotype (non‐brittle). The cross of parents with alternative mutations in the btr genes leads to a brittle F1 hybrid that presents grain retention problems. We evaluated rachis fragility through a mechanical test and under natural conditions, in F1 crosses with different compositions at the btr genes. Brittleness was significantly higher in Btr1btr1Btr2btr2 crosses compared to hybrids and inbred parents carrying one of the mutations (btr1btr1Btr2Btr2/Btr1Btr1btr2btr2). This fact could jeopardize the efficient harvest of hybrids bearing alternative mutations, reducing the choice of possible crosses for hybrid barley breeding and hindering the exploitation of potential heterotic patterns. Furthermore, non‐brittle hybrids showed higher brittleness than inbreds, suggesting the presence of other dominant factors affecting the trait. In conclusion, this work encourages a deeper study of the genetic control of the rachis brittleness trait and urges the consideration of rachis tenacity as a target for hybrid barley breeding.This work was supported by the Spanish Ministry of Economy, Industry and Competitiveness grants RFP2015 00006‐00‐00, and RTA2012‐00033‐C03‐02, and by the contract “Iberia region hybrid barley variety development and understanding effects of adaptation genes in hybrids,” between CSIC and Syngenta Crop Protection AG, which included funding for MFC PhD scholarship

Diversity and Relationships among U.S. Maize Inbreds Revealed by Restriction Fragment Length Polymorphisms

Restriction fragment length polymorphisms (RFLPs) have been proposed as molecular markers for characterizing the genetic diversity in maize (Zea mays L.). The objectives of this study were to evaluate the usefulness of RFLP data for (i) elucidating heterotic patterns among maize inbreds and (ii) assessing genetic similarity among related and unrelated lines. Thirty-two maize inbreds from the U.S. Corn Belt were analyzed for RFLPs with two restriction enzymes and 83 DNA probes distributed over the maize genome. Eighty-two probes detected polymorphisms with at least one enzyme. On average, 4.3 variants were found per probe-enzyme combination across all 32 inbreds. Genetic distances among lines, estimated from RFLP data as Rogers\u27 distance (RD), revealed considerable diversity among lines from Iowa Stiff Stalk Synthetic (BSSS), Reid Yellow Dent (RYD), and Lancaster Sure Crop (LSC). Lines from different heterotic groups had a slightly greater RD mean than unrelated lines from the same heterotic group, yet differences were small when compared with the wide range of RDs for individual lines combinations within each group. RDs between related lines agreed well with expectations based on coancestry coefficients determined from pedigree data with few exceptions. Principal component analyses of RFLP data resulted in a separate grouping of lines from BSSS/RYD and LSC. Dispersion of lines of miscellaneous origins was generally consistent with expectations based on known breeding behavior and pedigrees. Results from this study suggest that RFLP data can be used for assigning inbreds into heterotic groups and quantifying genetic similarity between related lines, but it seems that a large number of probe-enzyme combinations are required to obtain reliable estimates of genetic distance

Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers

Information about the genetic diversity and population structure in elite breeding material is of fundamental importance for the improvement of crops. The objectives of our study were to (a) examine the population structure and the genetic diversity in elite maize germplasm based on simple sequence repeat (SSR) markers, (b) compare these results with those obtained from single nucleotide polymorphism (SNP) markers, and (c) compare the coancestry coefficient calculated from pedigree records with genetic distance estimates calculated from SSR and SNP markers. Our study was based on 1,537 elite maize inbred lines genotyped with 359 SSR and 8,244 SNP markers. The average number of alleles per locus, of group specific alleles, and the gene diversity (D) were higher for SSRs than for SNPs. Modified Roger’s distance (MRD) estimates and membership probabilities of the STRUCTURE matrices were higher for SSR than for SNP markers but the germplasm organization in four heterotic pools was consistent with STRUCTURE results based on SSRs and SNPs. MRD estimates calculated for the two marker systems were highly correlated (0.87). Our results suggested that the same conclusions regarding the structure and the diversity of heterotic pools could be drawn from both markers types. Furthermore, although our results suggested that the ratio of the number of SSRs and SNPs required to obtain MRD or D estimates with similar precision is not constant across the various precision levels, we propose that between 7 and 11 times more SNPs than SSRs should be used for analyzing population structure and genetic diversity

Genetic diversity and linkage disequilibrium of two homologous genes to maize D8: sorghum SbD8 and pearl millet PgD8

Yield and yield stability of sorghum [Sorghum bicolor (L.) Moench.] and pearl millet [Pennisetum glaucum (L.) R.Br.] are highly influenced by flowering time and photoperiodic sensitivity in the arid to semi-arid regions of West and Central Africa. Photoperiodic sensitivity is the key adaptation trait of local landraces because it assures flowering at the end of the rainy season, independent of variable dates of planting. Flowering time genes are mainly integrated into four pathways with close interaction among each other: Vernalization, autonomous, GA (gibberellic acid) and photoperiod. In the GA pathway, maize D8, wheat RHT1 and rice SLR have been identified as homologous genes to the Arabidopsis GAI, which is a negative regulator of GA response. We have identified two homologous genes to D8: Sorghum SbD8 and pearl millet PgD8. These genes were expressed in the root and leaves of sorghum and pearl millet as revealed by EST database search and reverse transcription PCR, respectively. The genetic diversity of SbD8 was considerably lower than that of PgD8. The extent of linkage disequilibrium in PgD8 is lower than that of maize D8. SbD8 and PgD8 polymorphisms might be appropriate for dissection of photoperiod sensitivity using association mapping approaches

Root response to temperature extremes: association mapping of temperate maize (Zea mays L)

Little is known about the genetic control of the root architecture of maize (Zea mays L) and its response to temperature extremes. An association mapping panel, including 32 flint and 42 dent inbred lines, was characterized for root traits. The growth of axile and lateral roots was assessed non-destructively in growth pouches at 16°C (chilling), 28°C (control) and 36°C (heat). Association mapping was done using the PKOpt mixed-model associationmapping approach. Heat slowed down the development of seedling roots to a lesser extent than chilling, but differences between the heterotic groups were observed mainly at optimal temperature. Of 1,415 AFLP markers, 70 showed significant marker-trait associations and 90 showed significant marker-trait associations with temperature interaction effects. Compared to the flint lines, the dents showed stronger growth of axile roots, especially under optimal conditions, and carried more of the trait-increasing alleles for the length of axile roots. In contrast, Benjamin the flints accumulated more root dry weight at low temperature and exclusively carried the alleles favoring tolerance to chilling. A combination of inbreds carrying alleles positive for performance under contrasting temperature conditions should lead to a complementary effect in the hybrid and would increase adaptation to a wider range of temperature

Wheat genetic diversity trends during domestication and breeding

It has been claimed that plant breeding reduces genetic diversity in elite germplasm which could seriously jeopardize the continued ability to improve crops. The main objective of this study was to examine the loss of genetic diversity in spring bread wheat during (1) its domestication, (2) the change from traditional landrace cultivars (LCs) to modern breeding varieties, and (3) 50 years of international breeding. We studied 253 CIMMYT or CIMMYT-related modern wheat cultivars, LCs, and Triticum tauschii accessions, the D-genome donor of wheat, with 90 simple sequence repeat (SSR) markers dispersed across the wheat genome. A loss of genetic diversity was observed from T. tauschii to the LCs, and from the LCs to the elite breeding germplasm. Wheats genetic diversity was narrowed from 1950 to 1989, but was enhanced from 1990 to 1997. Our results indicate that breeders averted the narrowing of the wheat germplasm base and subsequently increased the genetic diversity through the introgression of novel materials. The LCs and T. tauschii contain numerous unique alleles that were absent in modern spring bread wheat cultivars. Consequently, both the LCs and T. tauschii represent useful sources for broadening the genetic base of elite wheat breeding germplasm

Genetic diversity among CIMMYT maize inbred lines investigated with SSR markers: II. subtropical, tropical midaltitude, and highland maize inbred lines and their relationships with elite U.S. and European maize

Characterization of genetic diversity of maize (Zea mays L.) germplasm is of great importance in hybrid maize breeding. The objectives of this study were to (i) investigate genetic diversity in CIMMYT subtropical, tropical midaltitude and highland inbreds with simple sequence repeat (SSR) markers, (ii) identify appropriate testers for the development of new inbred lines, (iii) compare this sample to U.S. and European elite maize lines and CIMMYT tropical lowland inbreds, and (iv) use the marker and pedigree information as a guide to understanding the heterotic relationship among the CIMMYT maize lines (CMLs) and their potential practical use in maize breeding programs worldwide. Inbreds included in the study were assayed with 79 SSR markers. The CIMMYT inbred lines originated from 35 mostly broad-based populations and pools with mixed origins. A total of 566 alleles were scored, (averaging 7.2 and ranging from 2 to 16 alleles per locus). The modified Roger's distance (MRD) between pairs of inbreds averaged 0.78, with a range of 0.45 to 0.93. Unweighted paired group method using arithmetic averages (UPGMA) cluster analysis revealed no clear clustering. This reflects a mixed composition of CIMMYT subtropical, tropical midaltitude and highland maize populations and pools, and indicates that large amounts of variation have been incorporated into CIMMYT germplasm. Temperate heterotic groups were separated based on the markers, and nontemperate CIMMYT maize was genetically distinct from temperate lines. Discrete clusters were difficult to identify within and often between megaenvironments. Specific recommendations for nontemperate hybrid maize breeding are made