Domestication has had a strong impact on the development of modern societies. We sequenced 200 genomes of the chocolate plant Theobroma cacao L. to show for the first time to our knowledge that a single population, the Criollo population, underwent strong domestication ~3600 years ago (95% CI: 2481–13,806 years ago). We also show that during the process of domestication, there was strong selection for genes involved in the metabolism of the colored protectants anthocyanins and the stimulant theobromine, as well as disease resistance genes. Our analyses show that domesticated populations of T. cacao (Criollo) maintain a higher proportion of high-frequency deleterious mutations. We also show for the first time the negative consequences of the increased accumulation of deleterious mutations during domestication on the fitness of individuals (significant reduction in kilograms of beans per hectare per year as Criollo ancestry increases, as estimated from a GLM, P = 0.000425).

Interspecific chromosome substitution is among the most powerful means of introgression and steps toward quantitative trait locus (QTL) identification. By reducing the genetic ''noise'' from other chromosomes, it greatly empowers the detection of genetic effects by specific chromosomes on quantitative traits. Here, we report on such results for 14 cotton lines (CS-B) with specific chromosomes or chromosome arms from G. barbadense L. substituted into G. hirsutum and chromosome-specific F 2 families. Boll size, lint percentage, micronaire, 2.5% span length, elongation, strength, and yield were measured by replicated field experiments in five diverse environments and analyzed under an additive-dominance (AD) genetic model with genotype and environment interaction. Additive effects were significant for all traits and dominance effects were significant for all traits except 2.5% span length. CS-B25 had additive effects increasing fiber strength and fiber length and decreasing micronaire. CS-B16 and CS-B18 had additive effects related to reduced yields. The results point toward specific chromosomes of G. barbadense 3-79 as the probable locations of the genes that significantly affect quantitative traits of importance. Our results provided a scope to analyze individual chromosomes of the genome in homozygous and heterozygous conditions and thus detected novel effects of alleles controlling important QTL.

are tandem repetitive DNA sequences. The availability and abundance of SSR markers throughout the cotton Knowledge of genetic diversity and relationships among breeding genome, their polymorphic nature, codominance, and materials has a significant impact on crop improvement. Association between parental divergence and progeny performance has not been polymerase chain reaction (PCR)-based assay make SSRs well documented in cotton (Gossypium hirsutum L.). The objectives useful in detecting genetic diversity (Reddy et al., 2001). of this study were to estimate genetic diversity among selected cotton The usefulness of GD as a predictor of hybrid perforgenotypes on the basis of simple sequence repeat (SSR) markers, and mance has been studied in several crops. In maize (Zea to investigate the relationship between genetic diversity and F 2 -bulk mays L.) and sunflower (Helianthus annuus L.), signifipopulation performance. Five U.S. and four Australian cultivars, and cant correlations between GD and hybrid performance two day-neutral converted lines of G. hirsutum were genotyped by were observed by Lee et al. (1989), Smith et al. (1990), means of 90 SSR primer pairs providing 69 polymorphic marker loci. Genetic distance (GD) between genotypes ranged from 0.06 to 0.34 Godshalk et al. (1990) and Dudley et al. (1991) observed for the 11 parental genotypes. The highest GD (0.34) was observed weak correlations between marker genotype and hybrid between ST474 and the day-neutral converted line B1388. The lowest GD (0.06) was detected between cultivars FM832 and FM975. The

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