Genomic Changes in Response to 110 Cycles of Selection for Seed Protein and Oil Concentration in Maize

Lucas, Christine J.; Zhao, Han; Schneerman, M. C.; Moose, Stephen P.

doi:10.1002/9781118525524.ch12

Cited by 19 publications

(14 citation statements)

References 65 publications

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“…This finding suggests that polygenic adaptation, in addition to major alleles, is likely to make an important contribution to adaptation in A. thaliana . This is consistent with earlier experimental findings on studies of artificial selection responses, where it has been shown that selection on many loci can lead to extreme adaptations in, for example, seed protein and kernel oil in maize (Laurie et al., ; Lucas, Zhao, Schneerman, & Moose, ), and body weight in mice (Allan, Eisen, & Pomp, ) and chicken (Besnier et al., ; Johansson, Pettersson, Siegel, & Carlborg, ; Sheng et al., ; Wahlberg et al., ).…”

Section: Discussionsupporting

confidence: 90%

A multilocus association analysis method integrating phenotype and expression data reveals multiple novel associations to flowering time variation in wild‐collected Arabidopsis thaliana

Zan

Carlborg

2018

Molecular Ecology Resources

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The adaptation to a new habitat often results in a confounding between genomewide genotype and beneficial alleles. When the confounding is strong, or the allelic effects is weak, it is a major statistical challenge to detect the adaptive polymorphisms. We describe a novel approach to dissect polygenic traits in natural populations. First, candidate adaptive loci are identified by screening for loci directly associated with the adaptive trait or the expression of genes known to affect it. Then, a multilocus genetic architecture is inferred using a backward elimination association analysis across all candidate loci with an adaptive false discovery rate-based threshold. Effects of population stratification are controlled by accounting for genomic kinship in both steps of the analysis and also by simultaneously testing all candidate loci in the multilocus model. We illustrate the method by exploring the polygenic basis of an important adaptive trait, flowering time in Arabidopsis thaliana, using public data from the 1,001 genomes project. We revealed associations between 33 (29) loci and flowering time at 10 (16)°C in this collection of natural accessions, where standard genomewide association analysis methods detected five (3) loci. The 33 (29) loci explained approximately 55.1 (48.7)% of the total phenotypic variance of the respective traits. Our work illustrates how the genetic basis of highly polygenic adaptive traits in natural populations can be explored in much greater detail using new multilocus mapping approaches taking advantage of prior biological information, genome and transcriptome data.

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Section: Discussionsupporting

confidence: 90%

A multilocus association analysis method integrating phenotype and expression data reveals multiple novel associations to flowering time variation in wild‐collected Arabidopsis thaliana

Zan

Carlborg

2018

Molecular Ecology Resources

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“…Although most of the unique alleles detected at C 0 in each composite were lost at C 4 possibly due to selection for favourable combination of alleles, their presence at low frequencies in advanced selection cycle of particularly TZL COMP4 is desirable for sustainable response from selection (Lucas et al. ) and as important source of novel alleles of desirable traits that can be used to broaden the genetic base of maize breeding populations (Pinto et al. ).…”

Section: Discussionmentioning

confidence: 99%

“…After four cycles of RRS, the proportion of alleles occurring at low frequencies decreased with selection consistent with the report of Pinto et al (2003a). Although most of the unique alleles detected at C 0 in each composite were lost at C 4 possibly due to selection for favourable combination of alleles, their presence at low frequencies in advanced selection cycle of particularly TZL COMP4 is desirable for sustainable response from selection (Lucas et al 2013) and as important source of novel alleles of desirable traits that can be used to broaden the genetic base of maize breeding populations (Pinto et al 2003a). In contrast, Labate et al (1997) found that a large fraction of unique RFLP alleles remained at reasonable frequencies in Iowa Stiff Stalk Synthetic and Iowa Corn Borer Synthetic after 12 cycles of RRS.…”

Section: Discussionmentioning

confidence: 99%

Genetic divergence in two tropical maize composites after four cycles of reciprocal recurrent selection

et al. 2017

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Two tropical maize composites were subjected to four cycles of reciprocal recurrent selection to develop divergent inbred lines with good combining ability. This study was conducted to examine the extent of genetic diversity, changes in allele composition and genetic structure, of 100 randomly selected S1 lines each from the original (C0) and advanced (C4) selection cycles of TZL COMP3 and TZL COMP4, genotyped using single nucleotide polymorphism (SNP) markers. Results revealed that the proportion of alleles at both low and high frequencies decreased from C0 to C4, whereas those at intermediate frequencies increased at C4 in the two composites. More unique and other alleles were lost at C4 in TZL COMP3 relative to those in TZL COMP4. The changes in different measures of genetic diversity were either small or negligible with selection in the two composites. The proportion of markers departing from Hardy–Weinberg equilibrium (HWE) decreased with selection, whereas the total number of pairs of markers in linkage disequilibrium increased with selection in the two composites. Examination of changes in population structures using a model‐based approach as well as cluster and multivariate analyses found a high degree of concordance in stratifying the 400 S1 lines into four non‐overlapping groups corresponding to the two selection cycles each within the reciprocal composites. The observed molecular‐based divergence between cycles within the same composite and the clear differentiation between the complementary composites highlight the importance of reciprocal recurrent selection for preserving genetic diversity for long‐term selection. This increases the potential of the advanced selection cycles to sustain genetic gain in productivity of hybrids adapted to the savannas in West and Central Africa.

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“…Initiated in 1896, this experiment aimed at selecting an open-pollinated variety for kernel protein and oil content in two directions, low and high value of each trait. The observed response to selection has been steady over time indicating no exhaustion of variability [ 35 ]. In flour beetles, continuous selection over 130 generations on pupa weight, starting from a heterogeneous background, has also resulted in constant increase of phenotypic value with a small decline in genetic variance.…”

Section: Introductionmentioning

confidence: 99%

Dearth of polymorphism associated with a sustained response to selection for flowering time in maize

Durand

Tenaillon

Raffoux³

et al. 2015

BMC Evol Biol

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BackgroundLong term selection experiments bring unique insights on the genetic architecture of quantitative traits and their evolvability. Indeed, they are utilized to (i) monitor changes in allele frequencies and assess the effects of genomic regions involved traits determinism; (ii) evaluate the role of standing variation versus new mutations during adaptation; (iii) investigate the contribution of non allelic interactions. Here we describe genetic and phenotypic evolution of two independent Divergent Selection Experiments (DSEs) for flowering time conducted during 16 years from two early maize inbred lines.ResultsOur experimental design uses selfing as the mating system and small population sizes, so that two independent families evolved within each population, Late and Early. Observed patterns are strikingly similar between the two DSEs. We observed a significant response to selection in both directions during the first 7 generations of selection. Within Early families, the response is linear through 16 generations, consistent with the maintenance of genetic variance. Within Late families and despite maintenance of significant genetic variation across 17 generations, the response to selection reached a plateau after 7 generations. This plateau is likely caused by physiological limits. Residual heterozygosity in the initial inbreds can partly explain the observed responses as evidenced by 42 markers derived from both Methyl-Sensitive Amplification- and Amplified Fragment Length- Polymorphisms. Among the 42, a subset of 13 markers most of which are in high linkage disequilibrium, display a strong association with flowering time variation. Their fast fixation throughout DSEs’ pedigrees results in strong genetic differentiation between populations and families.ConclusionsOur results reveal a paradox between the sustainability of the response to selection and the associated dearth of polymorphisms. Among other hypotheses, we discuss the maintenance of heritable variation by few mutations with strong epistatic interactions whose effects are modified by continuous changes of the genetic background through time.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0382-5) contains supplementary material, which is available to authorized users.

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Genomic Changes in Response to 110 Cycles of Selection for Seed Protein and Oil Concentration in Maize

Cited by 19 publications

References 65 publications

A multilocus association analysis method integrating phenotype and expression data reveals multiple novel associations to flowering time variation in wild‐collected Arabidopsis thaliana

A multilocus association analysis method integrating phenotype and expression data reveals multiple novel associations to flowering time variation in wild‐collected Arabidopsis thaliana

Genetic divergence in two tropical maize composites after four cycles of reciprocal recurrent selection

Dearth of polymorphism associated with a sustained response to selection for flowering time in maize

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