Flowering time is a complex trait that controls adaptation of plants to their local environment in the outcrossing species Zea mays (maize). We dissected variation for flowering time with a set of 5000 recombinant inbred lines (maize Nested Association Mapping population, NAM). Nearly a million plants were assayed in eight environments but showed no evidence for any single large-effect quantitative trait loci (QTLs). Instead, we identified evidence for numerous small-effect QTLs shared among families; however, allelic effects differ across founder lines. We identified no individual QTLs at which allelic effects are determined by geographic origin or large effects for epistasis or environmental interactions. Thus, a simple additive model accurately predicts flowering time for maize, in contrast to the genetic architecture observed in the selfing plant species rice and Arabidopsis.

Maize genetic diversity has been used to understand the molecular basis of phenotypic variation and to improve agricultural efficiency and sustainability. We crossed 25 diverse inbred maize lines to the B73 reference line, capturing a total of 136,000 recombination events. Variation for recombination frequencies was observed among families, influenced by local (cis) genetic variation. We identified evidence for numerous minor single-locus effects but little two-locus linkage disequilibrium or segregation distortion, which indicated a limited role for genes with large effects and epistatic interactions on fitness. We observed excess residual heterozygosity in pericentromeric regions, which suggested that selection in inbred lines has been less efficient in these regions because of reduced recombination frequency. This implies that pericentromeric regions may contribute disproportionally to heterosis.

Recombination is a crucial component of evolution and breeding, producing new genetic combinations on which selection can act. Rates of recombination vary tremendously, not only between species but also within species and for specific chromosomal segments. In this study, by examining recombination events captured in recombinant inbred mapping populations previously created for maize, wheat, Arabidopsis, and mouse, we demonstrate that substantial variation exists for genomewide crossover rates in both outcrossed and inbred plant and animal species. We also identify quantitative trait loci (QTL) that control this variation. The method that we developed and employed here holds promise for elucidating factors that regulate meiotic recombination and for creation of hyperrecombinogenic lines, which can help overcome limited recombination that hampers breeding progress.A LTHOUGH natural selection is a powerful evolutionary process, it utilizes only the existing variation present in a population. Recombination of alleles is required to efficiently evolve new genetic varieties. Not surprisingly, theoretical predictions (Otto and Michalakis 1998) and empirical studies (Saleem et al. 2001) indicate that populations experiencing directional or strong selection pressures evolve increased recombination rates. Similarly to the natural evolutionary processes, combining many positive alleles into a single germplasm is the main objective of plant and animal breeding. The stacking of the favorable alleles is limited by the time and the number of meioses required to recombine numerous alleles from multiple parents. Consequently, a better understanding of the factors controlling recombination holds numerous implications for both academic and applied realms.To date, many of the genes involved in meiotic recombination have been identified and the mechanistic basis of recombination have begun to emerge (Krogh and Symington 2004;Cohen et al. 2006;Li and Ma 2006). However, the mechanisms that regulate recombination are poorly understood. Particularly, little is known about the control of genomewide recombination rates. Variation in recombination rates has been documented both within and between species, as well as between particular chromosomal regions (Rees 1961;Säll 1990;Beavis and Grant 1991;Tulsieram et al. 1992;Fatmi et al. 1993;Korol et al. 1994;Williams et al. 1995;Sanchez-Moran et al. 2002;Anderson et al. 2003;De Massy 2003;Myers et al. 2005; YandeauNelson et al. 2006). A minimum of one obligatory crossover per chromosome, or chromosome arm, occurs during meiosis as a requirement for proper chromosome segregation (Pardo-Manuel De Villena and Sapienza 2001). However, factors that control whether just this one or multiple crossovers occur per chromosome are poorly understood. Even though the idea that recombination frequencies can be genetically dissected, as any other quantitative trait, was first proposed long ago (Rasmusson 1927), to our knowledge, no quantitative trait loci (QTL) affecting recombination rates have been ...

SummaryDespite their unsuitability for agricultural production, the wild relatives of crop species represent a largely untapped resource of novel QTLs potentially useful for crop plant improvement. In this regard, previous introgression studies, involving several different wild tomato species, have shown that the long arm of chromosome 4 contains QTLs for many horticulturally important traits including soluble solids content, fruit shape, lycopene content and biochemical composition. However, these earlier studies were unable to determine how many genes control these traits and whether genes affecting the same character from different wild species are allelic or not. In an effort to shed light on these issues, we have constructed a series of lines containing small, overlapping introgressions for portions of the long arm of chromosome 4 from L. peruvianum and L. hirsutum and tested these lines in replicated field trials. The results provide evidence for multiple, non-allelic loci controlling soluble solids and fruit weight. They also show that the loci controlling some traits (e.g. fruit shape, fruit weight, epidermal reticulation) co-localize to the same portions of chromosome 4, a result that may be attributed to pleiotropy and/or gene dense areas with lower than average recombination. The implications of these finding for molecular breeding and utilization of exotic germplasm are discussed.

Abstract:The near-isogenic line (NIL) TA1150 contains a 56-cM introgression from Lycopersicon chmielewskii chromosome 1 and has several interesting phenotypic characteristics including fruit with orange color, high levels of soluble solids, thick pericarp, small stem scars, and good firmness. A set of overlapping recombinant lines (subNILs) was developed and field tested to fine map the quantitative trait loci (QTL) controlling these traits. The results indicated that the solids, pericarp thickness, and firmness QTL are distinct from the color locus. Several of the QTL mapped in this study, including the soluble-solids QTL, probably correspond to QTL mapped in other wild species of tomato. However, analysis of a set of TA523 subNILs containing complementary introgressions from Lycopesicon hirsutum chromosome 1 suggests that this wild species may contain a different locus for improved soluble solids. Thus, it might be possible to combine the L. chmielewskii and L. hirsutum alleles for these loci in a single line with the potential for extremely highly soluble solids. The TA1150 subNIL TA1688 contains the smallest introgression of the solids locus (approximately 19 cM), as well as the pericarp thickness and firmness QTL, with a yield that was equivalent to two of the three control lines. Isolation of recombinant subNILs from TA1688 should break the linkage between orange color and high solids and provide a small introgressed segment for marker-assisted breeding and genetic improvement of processing tomato.Key words: tomato, QTL, soluble solids, Brix, colour.Résumé : La lignée quasi-isogénique (NIL) TA1150 contient un segment de 56 cM introgressé à partir du chromosome 1 du Lycopersicon chmielewskii et elle présente de nombreuses caractéristiques phénotypiques intéressantes dont des fruits orange, une forte teneur en solides solubles, un péricarpe épais, de petites cicatrices axillaires et une bonne fermeté. Des lignées recombinantes chevauchantes (subNIL) ont été développées et évaluées au champ pour réaliser une cartographie fine des locus à caractère quantitatif (QTL) contrôlant ces caractéristiques. Les résultats indiquent que les QTL pour les solides, l'épaisseur du péricarpe et la fermeté sont différents de ceux contrôlant la couleur. Plusieurs des QTL qui ont été localisés au cours de cette étude, dont les QTL pour les solides solubles, correspondent vraisemblablement à des QTL identifiés chez d'autres espèces de tomate sauvages. Cependant, une analyse de subNIL du TA523 qui comprend des introgressions supplémentaires du chromosome 1 du Lycopesicon hirsutum suggère que cette espèce pourrait contenir un locus différent pour ce qui est de la teneur en solides solubles. Ainsi, il pourrait s'avérer possible de combiner les allèles du L. chmielewskii et du L. hirsutum pour ces deux locus chez une seule lignée, laquelle pré-senterait potentiellement une très forte teneur en solides solubles. La subNIL TA1688 de la lignée TA1150 contient la plus petite introgression du locus des solides solubles (environ 19 cM) de ...