Root galling index (GI) and egg production (LogEGR) of <i>Meloidogyne incognita</i> on susceptible (TM-1, Pima 3–79, Pima S-7 and Acala SJ-2) and resistant (Acala N901 and Acala NemX) cotton cultivars.

<p>Data were collected 60 days after inoculation. The error bars show standard error.</p

QTLs associated by nonparametric mapping with root-galling index (GI) and nematode egg production (EGR) in TM-1 x Pima 3–79 RIL population.

a<p>QTL - Root-galling index (GI) phenotype;</p>b<p>QTL- Data for nematode egg production were transformed to Log₁₀(x+1) for analysis (Log EGR);</p>c<p>Chr: Cotton chromosome designation;</p>d<p><i>Mi-GI_h-C03₁</i>: The name of first (1) identified QTL for GI on chr 3 from <i>G. hirsutum</i> (h) to root-knot nematode <i>Meloidogyne incognita</i> (<i>Mi</i>): <i>Mi-EGR_b-C23</i>: The name of QTL for EGR on chr 23 from <i>G. barbadense (b)</i> to root-knot nematode <i>Meloidogyne incognita</i> (<i>Mi</i>);</p>e<p>K*: Kruskal-Wallis analysis test regarded as the nonparametric equivalent of the one-way analysis of variance (Van Ooijen 2004);</p>f<p><i>P</i>-value: P-values are designated as P<0.05 (**), 0.01 (***), 0.005 (****), 0.001 (*****), 0.0005 (******);</p>g<p>TM-1 <b>allele</b>: Mean value of phenotype associated with the TM-1 allele; Pima 3–79 allele, Mean value of phenotype associated with the Pima 3–79 allele.</p

Map locations of QTLs associated with resistance to root-knot nematode.

<p>Single-marker analysis conducted using nonparametric mapping (Kruskal-Wallis analysis) test equivalent of the one-way analysis of variance (Van Ooijen 2004). Red bars - QTL influencing root-galling index phenotype; Green bars - QTL influencing egg production phenotype (For Experiment I).</p

Effect of the combinations of QTLs for galling index and nematode egg production on mean phenotypic value (± standard error) based on genotypic classes carrying one to four favorable alleles (+, ++, +++, ++++ blue bars) and null genotypes (−,−−,−−−,−−−−, red bars) for Experiment I.

<p>Effect of the combinations of QTLs for galling index and nematode egg production on mean phenotypic value (± standard error) based on genotypic classes carrying one to four favorable alleles (+, ++, +++, ++++ blue bars) and null genotypes (−,−−,−−−,−−−−, red bars) for Experiment I.</p

Molecular Data Scores for G. hirsutum and G. barbadense

SSR fragment presence/absence matrix of molecular data originally collected from 1971 G. hirsutum and G. barbadense accessions obtained from the US National Cotton Germplasm Collection (NCGC) using 105 SSR markers. Please see ReadMe file for further information

A schematic diagram representing MTP based BAC-pool sequencing for complex genomes.

<p>454 and Sanger hybrid sequencing approach was used to derive high quality sequence assemblies in allotetraploid cotton.</p

Diagrammatic representation of BAC-pools and their homology across the pools and respective BAC clone ABI assemblies in Ctg-3301 and Ctg-465.

<p>Diagrammatic representation of BAC-pools and their homology across the pools and respective BAC clone ABI assemblies in Ctg-3301 and Ctg-465.</p

Comparative genomic analysis of Ctg-3301 (Chromosome A12) and Ctg-465 (Chromosome D12) of Upland cotton with <i>Arabidopsis</i> genome.

<p>Comparative genomic analysis of Ctg-3301 (Chromosome A12) and Ctg-465 (Chromosome D12) of Upland cotton with <i>Arabidopsis</i> genome.</p

Genetic linkage map of the F₃ population showing the location of QTL for photoperiodic flowering.

<p>Genetic linkage map of the F₃ population showing the location of QTL for photoperiodic flowering.</p

The level of polymorphism of all SSR markers between parental genotypes.

<p>The level of polymorphism of all SSR markers between parental genotypes.</p