Insights into the Effects of Long-Term Artificial Selection on Seed Size in Maize

Abstract

Grain produced from cereal crops is a primary source of human food and animal feed worldwide. To understand the genetic basis of seed-size variation, a grain yield component, we conducted a genome-wide scan to detect evidence of selection in the maize Krug Yellow Dent long-term divergent seed-size selection experiment. Previous studies have documented significant phenotypic divergence between the populations. Allele frequency estimates for 3 million single nucleotide polymorphisms (SNPs) in the base population and selected populations were estimated from pooled whole-genome resequencing of 48 individuals per population. Using F ST values across sliding windows, 94 divergent regions with a median of six genes per region were identified. Additionally, 2729 SNPs that reached fixation in both selected populations with opposing fixed alleles were identified, many of which clustered in two regions of the genome. Copy-number variation was highly prevalent between the selected populations, with 532 total regions identified on the basis of read-depth variation and comparative genome hybridization. Regions important for seed weight in natural variation were identified in the maize nested association mapping population. However, the number of regions that overlapped with the long-term selection experiment did not exceed that expected by chance, possibly indicating unique sources of variation between the two populations. The results of this study provide insights into the genetic elements underlying seed-size variation in maize and could also have applications for other cereal crops.G RAIN produced by cereal crops is a staple food source in many regions of the world in terms of direct human consumption and as an animal feed source. Understanding the molecular mechanisms underlying cereal grain yield and exploiting that knowledge through improved cultivars is essential to providing a stable food source to an ever-growing human population. Yield-component traits are of particular interest, as they generally have a higher heritability than grain yield per se (Austin and Lee 1998). For example, increasing seed size has been hypothesized as one method for increasing grain yield in cereal crops (Odhiambo and Compton 1987;Kesavan et al. 2013), and positive correlations between seed size and grain yield have been shown in maize (Peng et al. 2011) as well as other cereals such as Sorghum bicolor (L.) Moench (Yang et al. 2010). Maize is a prime species with which to explore natural and artificial variation related to grain-yield and yield-component traits in the cereals, as it is the most widely grown cereal crop worldwide and has vast genetic resources for probing the genetic basis of seed traits. The maize seed is composed of the embryo and endosperm that develop from double fertilization, the aleurone, which is an epidermal layer that covers the endosperm, and the maternal pericarp tissue. The endosperm, the primary storage component of the seed in maize, consists primarily of starch, while the embryo is high in oil conte...

The Conserved and Unique Genetic Architecture of Kernel Size and Weight in Maize and Rice

“…This indicates that the cis-element near ZmSLG might regulate its expression to affect kernel development. Notably, ZmSLG also is located within a region that has been shown to be under artificial selection during the generation of small seed and big seed populations by Hirsch et al (2014a). These results provide evidence that some maize orthologous genes might have similar and conserved functions as their rice counterparts.…”

The Genomic Impacts of Drift and Selection for Hybrid Performance in Maize

“…The lack of distinct selection signals in broad germplasm collections may be due to population-specific selection within germplasm subgroups; in this case, selection should be easier to detect in populations maintained in an individual program. This possibility is supported by the measured success in identifying targets of selection in individual experimental populations under directional selection for specific phenotypes such as seed size and ear number Hirsch et al 2014).In this study, we examine a different experiment in which the method and target of selection-reciprocal recurrent selection for hybrid yield-closely mirror those used in the generation of modern maize hybrids (Comstock et al 1949;Duvick et al 2004). Reciprocal recurrent selection is a method, initially proposed by Comstock et al (1949), in which lines from two populations are evaluated based on the phenotype of the hybrids each line produces when crossed with lines from the opposing population.…”

“…The lack of distinct selection signals in broad germplasm collections may be due to population-specific selection within germplasm subgroups; in this case, selection should be easier to detect in populations maintained in an individual program. This possibility is supported by the measured success in identifying targets of selection in individual experimental populations under directional selection for specific phenotypes such as seed size and ear number Hirsch et al 2014).…”

Selection Signatures in Four Lignin Genes from Switchgrass Populations Divergently Selected for In Vitro Dry Matter Digestibility

“…Allele segregation patterns were used to indicate causal markers in crossing populations, while the association between the genetic variance and the phenotypic variance was used in linkage disequilibrium mapping. Detection of allele frequency (AF) changes has been implemented in studying adaptively or artificially divergent populations [14–17]. Considering the large sample size needed to account for high density genetic variances in the natural populations, bulking the extremely divergent samples could drastically reduce the genotyping cost, and have been exploited successfully to detect SNPs associated with phenotype divergence [18, 19].…”