Bnapus                  package:bim                  R Documentation

_C_r_o_s_s _s_t_r_u_c_t_u_r_e _f_o_r _c_o_m_p_l_e_t_e _B_r_a_s_s_i_c_a _n_a_p_u_s _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     Contains genotypes and phenotypes for Brassica napus study,
     including 0- 4- and 8-week vernalization, survival, and 19
     chromosomes.

_U_s_a_g_e:

     data(Bnapus)

_F_o_r_m_a_t:

     See 'read.cross' in 'library(qtl)' for format.

_D_e_t_a_i_l_s:

     Traits included are percent winter survival for 1992-3, 1993-4,
     1994-5, 1997-8, and 1999-2000 (surv92, surv93, surv94, surv97,
     surv99, respectively), and days to flowering after no
     vernalization (flower0), 4 weeks vernalization (flower4) or 8
     weeks vernalization (flower8). Percents are of plants alive in the
     Fall, taken from the middle of rows (totals unavailable). Days to
     flowering after transplant are averages over four replicates from
     a RCB design (values by block unavailable). First column has the
     trait name. The remaining columns identify individual DH line
     (302-455). 

     Marker genotype data for Major x Stellar double haploid (DH)
     population. Double haploids have the same relation of
     recombination to distance as backcrosses as there is just one
     meiosis tracked (in F1). However, DH are homozygous at every locus
     (usually mapped as RI0 lines). Marker genotypes are coded as M =
     Major, S = Stellar, - = missing. Data columns are

     *  chrom = <em>B. napus</em> chromosome (N1, N2, etc.)

     *  order = along chromosome

     *  cM d= istance from proximal end

     *  marker = marker name: E = AFLP; *ec, *tg, *wg = RFLP; *xxx =
        other markers from Arabidopsis: Lem, eru1, eru2, fad3, isoDia,
        isoIdh, isoPgi, isoLap, pr2, slg6, Aca1, cor15

     *  Remaining columns are for individual DH lines (identifier
        302-455).

_S_o_u_r_c_e:

     Thomas C. Osborn (<URL: mailto:tcosborn@facstaff.wisc.edu>),
     Department of Agronomy, UW-Madison (<URL:
     http://agronomy.wisc.edu>).

_R_e_f_e_r_e_n_c_e_s:

     *  <URL: http://www.stat.wisc.edu/~yandell/qtl/data/osborn/Bnapus>

     *  Ferreira ME, Satagopan J, Yandell BS, Williams PH, Osborn TC
        (1995) Mapping loci controlling vernalization requirement and
        flowering time in Brassica napus. Theor Appl Genet 90: 727-732.
        [original source and analysis]

     *  JM Satagopan, BS Yandell, MA Newton and TC Osborn (1996) Markov
        chain Monte Carlo approach to detect polygene loci for complex
        traits. Genetics 144: 805-816. <URL:
        http://www.genetics.org/cgi/content/abstract/144/2/805> [first
        MCMC for experimental crosses; analysis of B. napus N2=LG9; see
        'vern' data]

     *  Kole C, Thorman CE, Karlsson BH, Palta JP, Gaffney P, Yandell
        BS, Osborn TC (2001) Comparative mapping of loci controlling
        winter survival and related traits in oilseed Brassica rapa and
        B. napus. Molecular Breeding 1: 329-339. [refined map and
        reanalysis]

_S_e_e _A_l_s_o:

     'read.cross','plot.bim'

_E_x_a_m_p_l_e_s:

     data(Bnapus)

     summary(Bnapus)
     plot(Bnapus)
     ## Not run: 
     Bnapus.bim = run.bmapqtl(Bnapus,"log10flower8")
     ## End(Not run)

