Patterns of DNA sequence polymorphism along chromosome 1 of maize ( Zea mays ssp. mays L.)

Abstract

We measured sequence diversity in 21 loci distributed along chromosome 1 of maize (Zea mays ssp. mays L.). For each locus, we sequenced a common sample of 25 individuals representing 16 exotic landraces and nine U.S. inbred lines. The data indicated that maize has an average of one single nucleotide polymorphism (SNP) every 104 bp between two randomly sampled sequences, a level of diversity higher than that of either humans or Drosophila melanogaster. A comparison of genetic diversity between the landrace and inbred samples showed that inbreds retained 77% of the level of diversity of landraces, on average. In addition, Tajima's D values suggest that the frequency distribution of polymorphisms in inbreds was skewed toward fewer rare variants. Tests for selection were applied to all loci, and deviations from neutrality were detected in three loci. Sequence diversity was heterogeneous among loci, but there was no pattern of diversity along the genetic map of chromosome 1. Nonetheless, diversity was correlated (r ‫؍‬ 0.65) with sequence-based estimates of the recombination rate. Recombination in our sample was sufficient to break down linkage disequilibrium among SNPs. Intragenic linkage disequilibrium declines within 100 -200 bp on average, suggesting that genome-wide surveys for association analyses require SNPs every 100 -200 bp. Single nucleotide polymorphisms (SNPs) are valuable tools for mapping complex phenotypic traits. An SNP either can contribute directly to a phenotype or it can associate with a phenotype as a result of linkage disequilibrium (LD) (1). In either case, it is clear that successful utilization of SNPs requires detailed knowledge of patterns of genetic polymorphism throughout the genome, as well as an understanding of the evolutionary forces shaping those patterns. These forces include genomic factors, such as the distribution of recombination and mutation rates along chromosomes, and evolutionary factors, such as the history of natural selection and population demography (2).Thus far, SNPs have been surveyed extensively for evolutionary purposes in relatively few systems. The surveys have yielded four important observations about DNA sequence diversity. First, diversity varies among species; for example, Drosophila melanogaster (drosophila) is Ϸ8-to 13-fold more diverse at the DNA sequence level than humans (3). Second, the effects of natural selection and demography vary among species. Half of the loci examined in drosophila do not fit the neutral equilibrium model of evolution (4), but only 1 of 16 loci analyzed in humans deviates from the neutral model (2). Third, SNPs provide insights into population history and demography. In humans, for example, African populations contain more genetic diversity than non-African populations, and non-

Genome analyses and modelling the relationships between coding density, recombination rate and chromosome length

“…What is also interesting is the fact that close to the transition point the ends of chromosomes are under purifying selection while the central parts of chromosome are rather complement. This observation suggests that uneven distribution of recombination events along the chromosomes should be observed -the higher recombination rates in the subtelomeric regions and the lower recombination rates in the central parts of chromosomes which agrees with the data obtained from the experimental studies of recombination in different organisms (Kong et al, 2002;Nachman, 2002;Tenaillon et al 2002;Jensen-Seaman et al, 2004;Prachumwat et al 2004;Barton et al, 2008).…”

“…Furthermore, there are some rules for distribution of recombination events along the chromosomesthe frequency of recombination is higher in the subtelomeric regions than in the central parts of chromosomes. The last statement is true for both, accepted recombination events in the real eukaryotic chromosomes (Kong et al, 2002;Nachman, 2002;Tenaillon et al 2002;Jensen-Seaman et al, 2004;Prachumwat et al 2004;Barton et al, 2008) as well as for virtual chromosomes in the Monte Carlo computer simulations . In the computer models, the implemented recombination events were distributed evenly along the chromosomes but haploid gametes forming the surviving zygotes were produced by recombination at the ends of chromosomes rather than in the middle of chromosomes.…”

How closely does genetic diversity in finite populations conform to predictions of neutral theory? Large deficits in regions of low recombination

“…Nucleotide diversity across chromosomes is positively correlated with recombination rate in Drosophila (Begun and Aquadro, 1992;Shapiro et al, 2007;Kulathinal et al, 2008), humans (Hellmann et al, 2005), white-throated sparrows , tomatoes (Stephan and Langley, 1998) and maize (Tenaillon et al, 2001), but not in A. lyrata (Wright et al, 2006). In several Drosophila species, nucleotide diversity differs by B10-fold between regions of high and low recombination (Stephan et al, 1992;Aquadro et al, 1994;Begun et al, 2007).…”

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

“…In all eukaryotes studied so far, the distribution of COs is not homogeneous along the chromosomes (Lukaszewski and Curtis 1993;Tenaillon et al 2002;Saintenac et al 2009;Mayer et al 2012;Pan et al 2012;Choulet et al 2014;Choi and Henderson 2015;Mercier et al 2015). For cultivated crops, this implies a decrease of the breeding power in regions showing low CO rates (Rodgers-Melnick et al 2015).…”