Because structural variation in the inflorescence architecture of cereal crops can influence yield, it is interest to identify genes responsible for this variation. However, manual collection phenotypes be time consuming large populations needed conduct genome-wide association studies (GWAS) and difficult multidimensional traits such as volume. A semiautomated phenotyping pipeline, TIM (Toolkit Inflorescence Measurement), was developed used extract unidimensional features from images 1,064...

Plant breeders make selection decisions based on multiple traits, such as yield, plant height, flowering time, and disease resistance. A commonly used approach in multi-trait genomic is index selection, which assigns weights to different traits relative their economic importance. However, classical only optimizes genetic gain the next generation, requires some experimentation find that lead desired outcomes, has difficulty optimizing nonlinear breeding objectives. Multi-objective...

Abstract The efficiency of solar radiation interception contributes to the photosynthetic crop plants. Light is a function canopy architecture, including plant density; leaf number, length, width, and angle; azimuthal orientation. We report on ability some maize (Zea mays) genotypes alter orientations their leaves during development in coordination with adjacent Although upper canopies these retain typical alternate-distichous phyllotaxy maize, grow parallel those A genome-wide association...

Abstract Goiffon et al. introduce the optimal population value (OPV) as a new metric for genomic selection. OPV is based on maximum possible haploid value... Genomic selection (GS) identifies individuals inclusion in breeding programs sum of their estimated marker effects or values (GEBVs). Due to significant correlation between GEBVs and true values, this has resulted enhanced rates genetic gain compared traditional methods Three extensions GS, weighted (WGS), (OHV) selection, genotype...

Plants can produce different phenotypes when exposed to environments. Understanding the genetic basis of these plastic responses is crucial for crop breeding efforts. We discuss two recent studies that suggest yield plasticity in maize has been under selection but controlled by genes than yield.

Genomewide association studies (GWAS) are computationally demanding analyses that use large sample sizes and dense marker sets to discover associations between quantitative trait variation genetic variants. FarmCPU is a powerful new method for performing GWAS. However, its performance hampered by details of implementation reliance on the R programming language. In this paper, we present an efficient FarmCPU, called FarmCPUpp, retains user interface but improves memory management speed...

This perspective lays out a framework to enable the breeding of crops that can meet worldwide demand under challenges global climate change. Past work in various fields has produced multiple prediction methods contribute different plant objectives. Our proposed focuses on integration these into decision-support tools quantify effects objectives decisions made throughout pipeline. We discuss complementarities among with an emphasis utilize operations research and systems approaches help...

ABSTRACT Climate change is projected to decrease maize yields due warmer temperatures and their consequences. Studies using crop growth models (CGMs), however, have predicted that, through a combination of alterations planting date, flowering time, maturity, these yield losses can be mitigated or even reversed. Here, we examine three assumptions such studies: (1) that climate has driven historical phenological trends, (2) CGM ensembles provide unbiased estimates under high temperatures, (3)...

The accuracy of trait measurements greatly affects the quality genetic analyses. During automated phenotyping, measurement errors, i.e. differences between automatically extracted values and ground truth, are often treated as random effects that can be controlled by increasing population sizes and/or replication number. In contrast, there is some evidence errors may partially under control. Consistent with this hypothesis, we observed substantial nonrandom, contributions to for five maize...

Global climate change is increasing both average temperatures and the frequencies of extreme high temperatures. Past studies have documented a strong negative effect exposures to >30°C on hybrid maize yields. However, these could not disentangle genetic adaptation via artificial selection from changes in agronomic practices. Because most earliest hybrids are no longer available, side-by-side comparisons with modern under current field conditions generally impossible. Here, we report...

Trait introgression (TI) can be a time-consuming and costly task that typically requires multiple generations of backcrossing (BC). Usually, the aim is to introduce one or more alleles (e.g. QTLs) from single donor into an elite recipient, both which are fully inbred. This article studies potential advantages incorporating intercrossing (IC) TI programs when compared with relying solely on traditional BC framework. We simulate breeding pipeline using 3 previously proposed selection...

Abstract Genome-wide association studies (GWAS) are computationally demanding analyses that use large sample sizes and dense marker sets to discover associations between quantitative trait variation genetic variants. FarmCPU is a powerful new method for performing GWAS. However, its performance hampered by details of implementation reliance on the R programming language. In this paper we present an efficient FarmCPU, called FarmCPUpp, retains user interface but improves memory management...

Phenotypic plasticity describes a genotype's ability to produce different phenotypes in response environments. Breeding crops that exhibit appropriate levels of for future climates will be crucial meeting global demand, but knowledge the critical environmental factors is limited handful well-studied major crops. Using 727 maize (Zea mays L.) hybrids phenotyped grain yield 45 environments, we investigated genetic algorithm and two other methods identify determinants from large set candidate...

Phenotypic plasticity describes the ability of a genotype to produce different phenotypes in response environments. A key component for quantification phenotypic is set environmental variables that influence particular phenotype. These are typically selected using domain-specific knowledge or, when suitably small, exhaustive search. Two factors complicate these strategies. First, environments shifting and becoming more variable due global climate change which may introduce novel stresses not...