The association mapping technique is a useful tool for detecting markers linked to the genes underlying the variation of a trait among elite cultivars. To avoid false-positive results due to unrecognized population structure in the analyzed set of individuals, the subpopulations need to be identified. Fifty-four lettuce (Lactuca sativa L.) cultivars representing five horticultural types important in North America, together with six accessions from two wild species (Lactuca saligna L. and Lactuca serriola L.), were assayed for polymorphism with target region amplified polymorphism (TRAP) marker loci. The model-based clustering approach recognized three main subpopulations in cultivated lettuce that are well separated from wild species. Although the clustering based on molecular markers was generally in good agreement with horticultural types, some cultivars were classified differently or showed mixed origin. The effect of population structure on association mapping was tested on four traits with strong or weak correlation to the lettuce horticultural type and monogenic or polygenic mode of inheritance. Traits that were strongly correlated with lettuce types displayed many false-positive results when population structure was ignored, but the spurious associations disappeared when estimates of population structure or relative kinship (both based on molecular markers) were included in the statistical model. Using of horticultural types as covariate was not sufficient to control for spurious associations in the monogenic trait with strong correlation to lettuce types. The best approach to avoid spurious associations in lettuce association studies is to assess relatedness of accessions with molecular markers and to include this information into the statistical model.
Ivan Simko and Jinguo Hu
Ivan Simko, Ryan J. Hayes, Krishna V. Subbarao and Rebecca Grube Sideman
Ryan J. Hayes, Carlos H. Galeano, Yaguang Luo, Rudie Antonise and Ivan Simko
Fresh-cut lettuce (Lactuca sativa) packaged as salad mixes are increasingly popular to consumers but are highly perishable. Cultivars bred with extended shelf life could increase overall production efficiency by reducing the frequency of product replacement in the marketplace. Understanding the inheritance of shelf life is needed to develop efficient breeding strategies for this trait. A population of 95 recombinant inbred lines (RILs) from slow-decaying ‘Salinas 88’ × rapidly decaying ‘La Brillante’ was grown in four field experiments. Cut lettuce was evaluated for decay in modified atmosphere (MA) packages flushed with N2 or air (control). Correlations between field experiments ranged from 0.47 to 0.84 (P < 0.01). Three quantitative trait loci (QTL) for decay of cut lettuce were detected on linkage groups (LGs) 1, 4, and 9 with ‘Salinas 88’ alleles associated with slower decay. The QTL on LG 4 (qSL4) was a major determinant of decay explaining 40% to 74% of the total phenotypic variance of the trait. The greatest effect of this QTL was observed between 29 and 50 days after harvest. QTL × environment interactions contributed less than 14% to the total variation. RILs with the ‘Salinas 88’ allele of qSL4 had slower decay when packaged in air compared with N2, whereas no difference between air and N2 packaging was detected with the ‘La Brillante’ allele. A subset of RILs with either the ‘Salinas 88’ or ‘La Brillante’ allele of qSL4 was grown in two field experiments and evaluated for decay of whole heads. Genetic variation among RILs for whole-head decay was found but could not be attributed to qSL4. Decay of cut lettuce in ‘Salinas 88’ × ‘La Brillante’ is a highly heritable trait conditioned by a few QTL and phenotypic selection is likely to be effective. However, shelf life evaluations are time-consuming, destructive, and require large amounts of field-grown lettuce. Therefore, qSL4 is a good QTL to develop molecular markers for marker-assisted selection. The mechanism of decay controlled by qSL4 is unknown but appears to be specific to cut lettuce and may have allele specific interactions with packaging atmospheric compositions.
Ryan J. Hayes, Mark A. Trent, Beiquan Mou, Ivan Simko, Samantha J. Gebben and Carolee T. Bull
Baby leaf lettuce cultivars with resistance to bacterial leaf spot (BLS) caused by Xanthomonas campestris pv. vitians (Xcv) are needed to reduce crop losses. The objectives of this research were to assess the genetic diversity for BLS resistance in baby leaf lettuce cultivars and to select early generation populations of lettuce with BLS resistance. Greenhouse experiments using artificial Xcv inoculations were conducted to assess BLS resistance in 35 cultivars of 10 lettuce types used in baby leaf production and in F2 through F3:4 progeny from ‘Batavia Reine des Glaces’ (BLS-resistant, green leaf color) × ‘Eruption’ (BLS-susceptible, red leaf color). Higher disease severity was identified in red leaf and red romaine cultivars compared with other types, indicating the need to target these types for resistance breeding. Selection for BLS resistance and red-colored leaves was therefore conducted among 486 F2 plants, 38 F2:3 families, and two populations of F3:4 families from ‘Batavia Reine des Glaces’ × ‘Eruption’. Two populations were identified with uniform levels of BLS resistance equivalent to ‘Batavia Reine des Glaces’ and variable leaf morphology and color. These populations can be used by private and publicly employed lettuce breeders to select for diverse types of lettuce cultivars suitable for baby leaf production and with BLS resistance.