Segregation Analysis of SSR, SNP, and AFLP Markers in F2 Population of Solanum lycopersicum × S. arcanum (Analisis Segregasi Marka SSR, SNP, dan AFLP pada Populasi F2 Persilangan Solanum lycopersicum × S. arcanum)

Abstract

<p>Distorted marker segregation is a common phenomenon in interspecific cross of various crops. Previous mapping study of early<br />blight fungus (Alternaria solani) resistance loci showed 52% marker distortion in the genetic linkage map of 176 F2 progenies<br />derived from Solanum lycopersicum cv. Solentos × S. arcanum LA2157. The objectives of this study were to analyze in detail the<br />marker segregation in the map and to determine the cause of segregation distortion by calculating the allele and genotype<br />frequencies of each marker. Out of 371 mapped markers, 192 markers deviated from the expected Mendelian ratio of 1 : 2 : 1.<br />Distorted markers occurred in all chromosomes, ranging from 1% to 92%. Surplus of S. arcanum homozygotes contributed most<br />to the skewness (40%), followed by heterozygotes (18%), and S. lycopersicum homozygotes (5%). The allele frequencies of 152<br />markers deviated from the expected allele homogeneity frequency, indicating that their segregation might be affected by<br />gamethophytic selection. Sixty-one markers deviated from the expected F2 genotype frequency distribution, indicating that their<br />segregation might be influenced by zygotic selection. Thirty-seven of the distorted markers showed deviation from expected<br />frequencies of allele homogeneity and F2 genotype frequency distribution. Distorted markers can be retained in linkage analysis<br />since chromosomal regions containing distorted markers showed linkage with early blight fungus resistance loci. Further<br />identification of the mechanism contributing segregation distortion requires detailed and extensive mapping studies.</p>