Pablo A. Quijada

A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture

Although quantitative trait locus (QTL) mapping has been successful in describing the genetic architecture of complex traits, the molecular basis of quantitative variation is less well understood, especially in plants such as maize that have large genome sizes. Regulatory changes at the teosinte branched1 (tb1) gene have been proposed to underlie QTLs of large effect for morphological differences that distinguish maize (Zea mays ssp. mays) from its wild ancestors, the teosintes (Z. mays ssp. parviglumis and mexicana). We used a fine mapping approach to show that intergenic sequences ∼58–69 kb 5′ to the tb1 cDNA confer pleiotropic effects on Z. mays morphology. Moreover, using an allele-specific expression assay, we found that sequences >41 kb upstream of tb1 act in cis to alter tb1 transcription. Our findings show that the large stretches of noncoding DNA that comprise the majority of many plant genomes can be a source of variation affecting gene expression and quantitative phenotypes.

Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 2. Identification of alleles from unadapted germplasm

Unadapted germplasm may contain alleles that could improve hybrid cultivars of spring oilseed Brassica napus. Quantitative trait loci (QTL) mapping was used to identify potentially useful alleles from two unadapted germplasm sources, a Chinese winter cultivar and a re-synthesized B. napus, that increase seed yield when introgressed into a B. napus spring hybrid combination. Two populations of 160 doubled haploid (DH) lines were created from crosses between the unadapted germplasm source and a genetically engineered male-fertility restorer line (P1804). A genetically engineered male-sterile tester line was used to create hybrids with each DH line (testcrosses). The two DH line populations were evaluated in two environments and the two testcross populations were evaluated in three or four environments for seed yield and other agronomic traits. Several genomic regions were found in the two testcross populations which contained QTL for seed yield. The map positions of QTL for days to flowering and resistance to a bacterial leaf blight disease coincided with QTL for seed yield and other agronomic traits, suggesting the occurrence of pleiotropic or linked effects. For two hybrid seed yield QTL, the favorable alleles increasing seed yield originated from the unadapted parents, and one of these QTL was detected in multiple environments and in both populations. In this QTL region, a chromosome rearrangement was identified in P1804, which may have affected seed yield.

Quantitative trait loci for resistance to Sclerotinia sclerotiorum and its association with a homeologous non-reciprocal transposition in Brassica napus L.

Sclerotinia stem rot, caused by fungus Sclerotinia sclerotiorum, is one of the most devastating diseases in rapeseed (Brassica napus L.). We report the identification of Quantitative trait loci (QTL) involved in the resistance to S. sclerotiorum in two segregating populations of DH lines: the HUA population, derived from a cross between a partially resistant Chinese winter line (Hua dbl2) and a susceptible European spring line (P1804); and the MS population, derived from a partially resistant French winter cultivar (Major) and a susceptible Canadian spring cultivar (Stellar). A petiole inoculation technique and two scoring methods, days to wilt (DW) and stem lesion length (SLL), were used for the resistance assessment. A total of eight genomic regions affecting resistance were detected in the HUA population, with four of these regions affecting both measures of resistance. Only one region, which affected both measurements, was detected in the MS population. Individual QTL explained 6–22% of the variance. At five of the QTL from both populations, alleles from the resistant parent contributed to the resistance. QTL on N2 from the HUA population had the highest LOD score and R2 value and was detected for SLL in the first evaluation. The N12 resistance allele in Hua dbl2 was detected in a region containing a homeologous non-reciprocal transposition (HNRT) from the resistance-containing portion of N2. This result suggests that QTL in the N12.N2 HNRT enhanced the resistance of Hua dbl2 by increasing the dosage of resistance genes. The relationship of QTL from different genetic backgrounds and their associations with other agronomic traits are discussed.

Confirmation of QTL controlling seed yield in spring canola (Brassica napus L.) hybrids

Allelic effects observed in QTL discovery experiments must be confirmed to be useful in subsequent breeding efforts. Two QTL affecting seed yield of spring hybrid canola (Brassica napus L.) were previously identified in two populations of inbred backcross lines (IBLs) containing germplasm introgressed from a winter cultivar. The effects of favorable alleles at these QTL were retested by crossing two selected IBLs (M5 and M31) to three spring canola lines having different genetic backgrounds. Doubled haploid (DH) lines derived from each F1 were genotyped with RFLP markers flanking the QTL and grouped into the four possible QTL genotypes. For the first field experiment, DH lines derived by crossing the M5 line to one spring line were crossed to two female testers and evaluated as individual testcross progenies in one environment. QTL genotypes had large variances and were not significantly different. A second field experiment was conducted using the DH lines from the first experiment and two other sets of DH lines derived from the M31 line crossed to two different spring canola lines. Individual lines within each QTL genotype of each set were bulked and crossed to the same testers used in Experiment 1. Bulked hybrid seeds of each QTL genotype were planted in a split-split plot randomized block design and 12 replicates. QTL genotypes had smaller variances in this experiment, and the effects of one QTL were confirmed in some genetic backgrounds. These results suggest that bulking of QTL genotypes and use of an appropriate experimental design with many replicates are needed to detect small differences between QTL genotypes.