Genetic Effects of 1BS Chromosome Arm on the Main Agronomic Traits in Chuanmai 42

ABSTRACTHeterosis has been key to the development of maize breeding but describing its genetic basis has been challenging. Previous studies of heterosis have shown the contribution of within-locus complementation effects (dominance) and their differential importance across genomic regions. However, they have generally considered panels of limited genetic diversity and have shown little benefit to including dominance effects for predicting genotypic value in breeding populations. This study examined within-locus complementation and enrichment of genetic effects by functional classes in maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the United States (1,106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1,640 hybrids). We assayed three agronomic traits: days to silking (DTS), plant height (PH) and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results point to mechanisms by which heterosis arises through local complementation in proximal gene regions and suggest the relevance of dominance and gene annotations for genomic prediction in maize.

Download Full-text

Genetic effects of the critical factors of sugary1 fitness

The Journal of Agricultural Science ◽

10.1017/s0021859614001270 ◽

2015 ◽

Vol 154 (1) ◽

pp. 40-57

Author(s):

A. DJEMEL ◽

B. ORDÁS ◽

L. HANIFI-MEKLICHE ◽

L. KHELIFI ◽

A. ORDÁS ◽

...

Keyword(s):

Environmental Conditions ◽

Agronomic Traits ◽

Block Design ◽

Genetic Regulation ◽

Field Evaluation ◽

Field Trials ◽

Inbred Lines ◽

Genetic Effects ◽

Seedling Vigour ◽

Western Spain

SUMMARYThe present study was designed to estimate the effects of the mutant su1 on the genetic regulation of fitness-related traits when introgressed into field maize backgrounds. Estimated genetic effects of agronomic traits in Su1 v. su1 plants were monitored in two separate mean generation designs. The first involved unrelated inbred lines EP42 and A631, while two Corn Belt inbred lines, A619 and A632, were used for the second design. Parents, F1s, F2s and backcrosses were crossed to the su1 inbred P39 as the donor of su1 and the 12 crosses were successively self-pollinated for 5 years. For each cross, Su1 and su1 kernels were evaluated separately in a growth chamber under controlled environmental conditions following a randomized complete block design. In addition, the genotypes were evaluated in field trials in 10 × 10 triple lattice designs during 2010 and 2011 at Pontevedra in north-western Spain; and in 2010 at Algiers, located in the sub-humid North of Algeria. The performance of su1 plants was lower when compared to the Su1 plants for all traits evaluated in both designs and across environments. The estimates of genetic effects of Su1 v. su1 plants were strongly affected by genotype and environment. The results suggest that, depending on specific sweet × field maize interaction, seedling vigour and, particularly, chlorophyll content (CCM) were the most critical traits in determining su1 viability. However, the complexity of the genetic regulation of emergence and the great heterogeneity of environmental conditions in the field evaluation prevent the estimation of the genetic regulation on sugary1 fitness.

Download Full-text

A low resolution epistasis mapping approach to identify chromosome arm interactions in allohexaploid wheat

10.1101/377713 ◽

2018 ◽

Cited By ~ 1

Author(s):

Nicholas Santantonio ◽

Jean-Luc Jannink ◽

Mark E. Sorrells

Keyword(s):

Mixed Model ◽

Agronomic Traits ◽

Statistical Tests ◽

Covariance Matrices ◽

Low Resolution ◽

Model Framework ◽

Epistatic Interactions ◽

Epistatic Effects ◽

Chromosome Arm ◽

Homeologous Chromosome

1AbstractEpistasis is an important contributor to genetic variance, even in inbred populations where it is present as additive by additive interactions. Testing for epistasis presents a multiple testing problem as the search space for modest numbers of markers is large. Additionally, single markers do not necessarily track functional units of interacting chromatin as well as haplotype based methods do. To harness the power of multiple markers while drastically minimizing the number of tests conducted, we present a low resolution test for epistatic interactions across whole chromosome arms. Two additive genetic covariance matrices are constructed from markers on two different chromosome arms. The Hadamard product of these additive covariance matrices is then used to produce the additive by additive epistasis covariance matrix between the two chromosome arms. The covariance matrices are subsequently used to estimate an epistatic interaction variance parameter in a mixed model framework, while correcting for background additive and epistatic effects. We find significant epistatic interactions for 2% of interactions tested for four agronomic traits in a population of winter wheat. Interactions across homeologous chromosome arms were identified, but were less abundant than other interaction chromosome arm pairs. Of these, homeologous chromosome arm pair 4BL and 4DL showed a strong relationship between the product of their additive effects and the interaction effect that may be indicative of functional redundancy. Several chromosome arms were involved in many interactions across the genome, suggesting that they may contain important large effect regulatory factors. The differential patterns of epistasis across different traits suggests that detection of epistatic interactions is robust when correcting for background additive and epistatic effects in the population. The low resolution epistasis mapping method presented here identifies important epistatic interactions with a limited number of statistical tests at the cost of relatively lower precision.

Download Full-text