The domestic dog exhibits greater diversity in body size than any other terrestrial vertebrate. We used a strategy that exploits the breed structure of dogs to investigate the genetic basis of size. First, through a genome-wide scan, we identified a major quantitative trait locus (QTL) on chromosome 15 influencing size variation within a single breed. Second, we examined genetic variation in the 15-megabase interval surrounding the QTL in small and giant breeds and found marked evidence for a selective sweep spanning a single gene (IGF1), encoding insulin-like growth factor 1. A single IGF1 single-nucleotide polymorphism haplotype is common to all small breeds and nearly absent from giant breeds, suggesting that the same causal sequence variant is a major contributor to body size in all small dogs.

Coat color and type are essential characteristics of domestic dog breeds. Although the genetic basis of coat color has been well characterized, relatively little is known about the genes influencing coat growth pattern, length, and curl. We performed genome-wide association studies of more than 1000 dogs from 80 domestic breeds to identify genes associated with canine fur phenotypes. Taking advantage of both inter- and intrabreed variability, we identified distinct mutations in three genes, RSPO2, FGF5, and KRT71 (encoding R-spondin–2, fibroblast growth factor–5, and keratin-71, respectively), that together account for most coat phenotypes in purebred dogs in the United States. Thus, an array of varied and seemingly complex phenotypes can be reduced to the combinatorial effects of only a few genes.

The first genetic transcript map of the soybean genome was created by mapping one SNP in each of 1141 genes in one or more of three recombinant inbred line mapping populations, thus providing a picture of the distribution of genic sequences across the mapped portion of the genome. Singlenucleotide polymorphisms (SNPs) were discovered via the resequencing of sequence-tagged sites (STSs) developed from expressed sequence tag (EST) sequence. From an initial set of 9459 polymerase chain reaction primer sets designed to a diverse set of genes, 4240 STSs were amplified and sequenced in each of six diverse soybean genotypes. In the resulting 2.44 Mbp of aligned sequence, a total of 5551 SNPs were discovered, including 4712 single-base changes and 839 indels for an average nucleotide diversity of u ¼ 0.000997. The analysis of the observed genetic distances between adjacent genes vs. the theoretical distribution based upon the assumption of a random distribution of genes across the 20 soybean linkage groups clearly indicated that genes were clustered. Of the 1141 genes, 291 mapped to 72 of the 112 gaps of 5-10 cM in the preexisting simple sequence repeat (SSR)-based map, while 111 genes mapped in 19 of the 26 gaps .10 cM. The addition of 1141 sequence-based genic markers to the soybean genome map will provide an important resource to soybean geneticists for quantitative trait locus discovery and map-based cloning, as well as to soybean breeders who increasingly depend upon marker-assisted selection in cultivar improvement.

Soybean [Glycine max (L.) Merr.] yield, when regressed on water needed to replenish 0 to 100% seasonal evapotranspiration (ET), generates an estimate of season‐specific water‐use efficiency (WUE). The impact of unpredictable water deficits might be lessened if high‐yielding genotypes had a smaller beta. Our objective was to determine the genetic basis of beta and carbon isotope discrimination (CID), a theorized indicator of transpiration efficiency (TE). A ‘Minsoy’ × ‘Noir 1’ population of 236 recombinant inbred lines (RILs), genotyped at 665 loci, was evaluated in six water treatments (100, 80, 60, 40, 20, and 0% ET) for 2 yr. Water stress was mild in 1994, but high temperatures and no rainfall in 1995 led to a drought so severe that the 100% ET treatment required 41 cm of irrigation. The 1995 yield‐to‐water regression was highly linear (28 kg ha−1 cm−1). Genotype × water (G × W) interaction was due to genotypic heterogeneity in beta The CID vs. beta correlation was low (r = 0.26), so selection for better leaf TE may not improve crop WUE. Selection of low beta (less sensitivity to drought) will be difficult, given the yield beta vs. yield correlation (r = 0.71). The major quantitative trait loci (QTL) for yield beta, yield, and CID were coincident with maturity and/or determinancy QTLs, except for a CID QTL in linkage group U09‐C2, but it had no effect on beta Genetic improvement of soybean yield performance under drought would be better achieved by coupling a high‐yield grand mean with a high‐ (not low‐) yield beta

are homozygous and their genotypes can be reproduced by different research groups for repeated experiments Molecular markers provide a rapid approach to breeding for dein a variety of environments (Mather and Jinks, 1977). sired agronomic traits. To use them, it is necessary to determine the linkage between quantitative trait loci (QTLs) and such markers. The

Many agronomic traits of interest to plant breeders are quantitative. Recombinant inbred (RI) lines are particularly useful in genetic mapping studies of quantitative traits. A recombinant inbred population was derived from the Glycine max (L.) Merr. parents ‘Minsoy’ and ‘Noir 1’. This soybean population was used to investigate the genetic basis of several agronomic traits: days to flower (Rl), days to maturity (R8), reproductive period (RS‐R1), plant height, lodging score, height divided by lodging (the ability of tall plants to stand upright), seed protein content, seed oil content, seed size, yield, seed number, yield divided by height (the yield from short plants), leaf width, leaf length, and leaf area. In this RI population, transgressive segregation was observed for all of these traits. As expected, height and lodging were correlated, as were height and maturity; height and maturity with yield; and leaf length and width with leaf area. Height divided by lodging and yield divided by height showed little correlation with other traits, indicating that these traits measured new plant phenotypes. A genetic map was constructed for this population, with restriction fragment length polymorphism markers, simple sequence repeat markers and classical markers. Approximately 2000 cM of linkage was defined. The data were used to identify quantitative trait loci (QTLs) by linking quantitative phenotypes to qualitative genetic markers. for many traits, a few QTLs accounted for a large proportion of the variation observed. QTLs for most of the traits were associated with three linkage groups, often with the same genetic locus within the linkage group. At the level of resolution of the genetic map for this population, it was not possible to determine whether these QTLs have pleiotrophic effects or are clusters of separate, tightly linked genes. The data suggest that separation of QTLs for different traits (such as maturity or lodging and yield) may be difficult, but that this RI population will be useful in resolving questions concerning marker assisted selection of quantitative traits.

Phenotypic stereotypes are traits, often polygenic, that have been stringently selected to conform to specific criteria. In dogs, Canis familiaris, stereotypes result from breed standards set for conformation, performance (behaviors), etc. As a consequence, phenotypic values measured on a few individuals are representative of the breed stereotype. We used DNA samples isolated from 148 dog breeds to associate SNP markers with breed stereotypes. Using size as a trait to test the method, we identified six significant quantitative trait loci (QTL) on five chromosomes that include candidate genes appropriate to regulation of size (e.g., IGF1, IGF2BP2 SMAD2, etc.). Analysis of other morphological stereotypes, also under extreme selection, identified many additional significant loci. Less well-documented data for behavioral stereotypes tentatively identified loci for herding, pointing, boldness, and trainability. Four significant loci were identified for longevity, a breed characteristic not under direct selection, but inversely correlated with breed size. The strengths and limitations of the approach are discussed as well as its potential to identify loci regulating the within-breed incidence of specific polygenic diseases.

Evolution of mammalian skeletal structure can be rapid and the changes profound, as illustrated by the morphological diversity of the domestic dog. Here we use principal component analysis of skeletal variation in a population of Portuguese Water Dogs to reveal systems of traits defining skeletal structures. This analysis classifies phenotypic variation into independent components that can be used to dissect genetic networks regulating complex biological systems. We show that unlinked quantitative trait loci associated with these principal components individually promote both correlations within structures (e.g., within the skull or among the limb bones) and inverse correlations between structures (e.g., skull vs. limb bones). These quantitative trait loci are consistent with regulatory genes that inhibit growth of some bones while enhancing growth of others. These systems of traits could explain the skeletal differences between divergent breeds such as Greyhounds and Pit Bulls, and even some of the skeletal transformations that characterize the evolution of hominids.