B73-Mo17 Near-Isogenic Lines Demonstrate Dispersed Structural Variation in Maize

Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA.
Plant physiology (Impact Factor: 7.39). 06/2011; 156(4):1679-90. DOI: 10.1104/pp.111.174748
Source: PubMed

ABSTRACT Recombinant inbred lines developed from the maize (Zea mays ssp. mays) inbreds B73 and Mo17 have been widely used to discover quantitative trait loci controlling a wide variety of phenotypic traits and as a resource to produce high-resolution genetic maps. These two parents were used to produce a set of near-isogenic lines (NILs) with small regions of introgression into both backgrounds. A novel array-based genotyping platform was used to score genotypes of over 7,000 loci in 100 NILs with B73 as the recurrent parent and 50 NILs with Mo17 as the recurrent parent. This population contains introgressions that cover the majority of the maize genome. The set of NILs displayed an excess of residual heterozygosity relative to the amount expected based on their pedigrees, and this excess residual heterozygosity is enriched in the low-recombination regions near the centromeres. The genotyping platform provided the ability to survey copy number variants that exist in more copies in Mo17 than in B73. The majority of these Mo17-specific duplications are located in unlinked positions throughout the genome. The utility of this population for the discovery and validation of quantitative trait loci was assessed through analysis of plant height variation.

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Available from: Cheng-Ting Yeh, Jan 29, 2015
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    • "Genetic mapping has identified quantitative trait loci (QTL) that confer resistance to several maize-feeding insects, including Diatraea grandiosella (southwestern corn borer; Khairallah et al., 1998), Ostrinia nubilalis (European corn borer; Papst et al., 2004), Ostrinia furnacalis (Asian corn borer; Xia et al., 2010), Helicoverpa zea (corn earworm; Byrne et al., 1998), Spodoptera frugiperda (fall armyworm; Brooks et al., 2007), and Sitophilus zeamais (maize weevil, García-Lara et al., 2009). Discovery of the actual genetic basis of such insect resistance QTL has been facilitated by the genome sequence of maize inbred line B73 (Schnable et al., 2009), as well as by populations of recombinant inbred lines (RILs) and nearisogenic lines (NILs) that have been created from B73 and a diverse set of other maize inbred lines (Eichten et al., 2011; Lee et al., 2002; McMullen et al., 2009b; Yu et al., 2008). The proximal causes of natural variation in maize insect resistance have been linked to the production of defensive proteins and secondary metabolites. "
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    ABSTRACT: Plants show considerable within-species variation in their resistance to insect herbivores. In the case of Zea mays (cultivated maize), Rhopalosiphum maidis (corn leaf aphids) produce approximately twenty times more progeny on inbred line B73 than on inbred line Mo17. Genetic mapping of this difference in maize aphid resistance identified quantitative trait loci (QTL) on chromosomes 4 and 6, with the Mo17 allele reducing aphid reproduction in each case. The chromosome 4 QTL mapping interval includes several genes involved in the biosynthesis of DIMBOA (2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one), a maize defensive metabolite that also is required for callose accumulation in response to aphid feeding. Consistent with the known association of callose with plant defence against aphids, R. maidis reproduction on B73×Mo17 recombinant inbred lines was negatively correlated with both DIMBOA content and callose formation. Further genetic mapping, as well as experiments with near-isogenic lines, confirmed that the Mo17 allele causes increased DIMBOA accumulation relative to the B73 allele. The chromosome 6 aphid resistance QTL functions independently of DIMBOA accumulation and has an effect that is additive to that of the chromosome 4 QTL. Thus, at least two separate defence mechanisms account for the higher level of R. maidis resistance in Mo17 compared with B73.
    Journal of Experimental Botany 09/2014; 66(2). DOI:10.1093/jxb/eru379 · 5.79 Impact Factor
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    • "Validation of a strong-effect SAM height QTL We sought to validate the existence of SAM_height_6, a strong-effect QTL (16% variation explained, LOD 9.25) on chromosome 5 at 892.812895 cM (Table 3 and Table S5) using a set of three NILs (Eichten et al. 2011). Two NILs (B034 and B063) had a largely B73 genome with regions of Mo17 introgression whereas the other line (M049) was mostly Mo17 with at least one introgressed region of B73. "
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    ABSTRACT: The shoot apical meristem contains a pool of undifferentiated stem cells, and generates all above-ground organs of the plant. During vegetative growth, cells differentiate from the meristem to initiate leaves while the pool of meristematic cells is preserved; this balance is determined in part by genetic regulatory mechanisms. To assess vegetative meristem growth and genetic control in Zea mays, we investigated its morphology at multiple time points and identified three stages of growth. We measured meristem height, width, plastochron internode length, and associated traits from 86 individuals of the intermated B73 x Mo17 recombinant inbred line population. For meristem height-related traits, the parents exhibited markedly different phenotypes, with B73 being very tall, Mo17 short, and the population distributed between. In the outer cell layer, differences appeared to be related to number of cells rather than cell size. In contrast, B73 and Mo17 were similar in meristem width traits and plastochron internode length, with transgressive segregation in the population. Multiple loci (6-9 for each trait) were mapped, indicating meristem architecture is controlled by many regions; none of these coincided with previously described mutants impacting meristem development. Major loci for height and width explaining 16% and 19% of the variation were identified on chromosomes 5 and 8, respectively. Significant loci for related traits frequently coincided, while those for unrelated traits did not overlap. Using three near-isogenic lines, a locus explaining 16% of the parental variation in meristem height was validated. Published expression data were leveraged to identify candidate genes in significant regions.
    G3-Genes Genomes Genetics 05/2014; 4(7). DOI:10.1534/g3.114.011940 · 2.51 Impact Factor
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    • "Equation 2 was verified based on two QTL mapping experiments. The first experiment consisted of previously published data on plant height in the IBM population (Eichten et al. 2011), while the second was based on simulations for a nonintermated RI population of 250 individuals . In both cases, the optimal number of markers suggested by (2) was within 200 of the observed marker number that provided a maximally powerful test (Figure 5). "
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    ABSTRACT: Genotyping-by-sequencing (GBS) approaches provide low-cost, high-density genotype information. However, GBS has unique technical considerations including a substantial amount of missing data and a non-uniform distribution of sequence reads. The goal of this study was to characterize technical variation using this method and to develop methods to optimize read-depth to obtain desired marker coverage. To empirically assess the distribution of fragments produced using GBS, approximately 8.69 Gb of GBS data was generated on the Zea mays reference inbred B73 utilizing ApeKI for genome reduction and single-end reads between 75 and 81 bp in length. We observed wide variation in sequence coverage across sites. Approximately 76% of potentially observable cut site-adjacent sequence fragments had no sequencing reads whereas a portion had substantially greater read depth than expected, up to 2,369 times the expected mean. The methods described in this manuscript facilitate determination of sequencing depth in the context of empirically defined read-depth to achieve desired marker density for genetic mapping studies.
    Genetics 02/2013; 193(4). DOI:10.1534/genetics.112.147710 · 4.87 Impact Factor
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