a b s t r a c tIt is estimated that more than 95% of organic production is based on crop varieties that were bred for the conventional high-input sector. Recent studies have shown that such varieties lack important traits required under organic and low-input production conditions. This is primarily due to selection in conventional breeding programmes being carried out in the background of high inorganic fertilizer and crop protection inputs. Also, some of the traits (e.g., semi-dwarf genes) that were introduced to address problems like lodging in cereals in high-input systems were shown to have negative side-effects (reduced resistance to diseases such as Septoria, lower protein content and poorer nutrient-use efficiency) on the performance of varieties under organic and low-input agronomic conditions. This review paper, using wheat, tomato and broccoli as examples, describes (1) the main traits required under low-input conditions, (2) current breeding programmes for organic, low-input agriculture, (3) currently available breeding and/or selection approaches, and (4) the benefits and potential negative side-effects of different breeding methodologies and their relative acceptability under organic farming principles.
White mold, caused by Sclerotinia sclerotiorum, is a devastating fungal disease of common bean (Phaseolus vulgaris L.) worldwide. Physiological resistance and disease avoidance conferred by plant architecture-related traits contribute to white mold field resistance. Our objective was to further examine white mold disease avoidance in common bean. A comparative map composed of 79 quantitative trait loci (QTL) for white mold resistance (27), disease avoidance traits (36) and root traits (16) was generated. Thirteen white mold resistance QTL, six with strong and seven with weak associations with disease avoidance traits, were observed. Root length and lodging QTL co-located in three regions.
The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP) array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids) and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA) and pairwise estimates of F st supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S. pimpinellifolium. Further divisions were found within both the contemporary processing and fresh market sub-populations. These sub-populations showed higher levels of genetic diversity relative to the vintage sub-population. The array provided a large number of polymorphic SNP markers across each sub-population, ranging from 3,159 in the vintage accessions to 6,234 in the cultivated cherry accessions. Visualization of minor allele frequency revealed regions of the genome that distinguished three representative sub-populations of cultivated tomato (processing, fresh market, and vintage), particularly on chromosomes 2, 4, 5, 6, and 11. The PCA loadings and F st outlier analysis between these three sub-populations identified a large number of candidate loci under positive selection on chromosomes 4, 5, and 11. The extent of linkage disequilibrium (LD) was examined within each chromosome for these sub-populations. LD decay varied between chromosomes and sub-populations, with large differences reflective of breeding history. For example, on chromosome 11, decay occurred over 0.8 cM for processing accessions and over 19.7 cM for fresh market accessions. The observed SNP variation and LD decay suggest that different patterns of genetic variation in cultivated tomato are due to introgression from wild species and selection for market specialization.
White mold, caused by the fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a major disease that limits common bean production and quality worldwide. The host-pathogen interaction is complex, with partial resistance in the host inherited as a quantitative trait with low to moderate heritability. Our objective was to identify meta-QTL conditioning partial resistance to white mold from individual QTL identified across multiple populations and environments. The physical positions for 37 individual QTL were identified across 14 recombinant inbred bi-parental populations (six new, three re-genotyped, and five from the literature). A meta-QTL analysis of the 37 QTL was conducted using the genetic linkage map of Stampede x Red Hawk population as the reference. The 37 QTL condensed into 17 named loci (12 previously named and five new) of which nine were defined as meta-QTL WM1.1, WM2.2, WM3.1, WM5.4, WM6.2, WM7.1, WM7.4, WM7.5, and WM8.3. The nine meta-QTL had confidence intervals ranging from 0.65 to 9.41 Mb. Candidate genes shown to express under S. sclerotiorum infection in other studies, including cell wall receptor kinase, COI1, ethylene responsive transcription factor, peroxidase, and MYB transcription factor, were found within the confidence interval for five of the meta-QTL. The nine meta-QTL are recommended as potential targets for MAS for partial resistance to white mold in common bean.
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