A glabrous, yellow-seeded doubled haploid (DH) line and a hairy, black-seeded DH line in Chinese cabbage (B. rapa) were used as parents to develop a DH line population that segregated for both hairiness and seed coat color traits. The data showed that both traits completely co-segregated each other, suggesting that one Mendelian locus controlled both hairiness and seed coat color in this population. A fine genetic map was constructed and a SNP marker that was located inside a Brassica ortholog of TRANSPARENT TESTA GLABRA 1 (TTG1) in Arabidopsis showed complete linkage to both the hairiness and seed coat color gene, suggesting that the Brassica TTG1 ortholog shared the same gene function as its Arabidopsis counterpart. Further sequence analysis of the alleles from hairless, yellow-seeded and hairy, black-seeded DH lines in B. rapa showed that a 94-base deletion was found in the hairless, yellow-seeded DH lines. A nonfunctional truncated protein in the hairless, yellow-seeded DH lines in B. rapa was suggested by the coding sequence of the TTG1 ortholog. Both of the TTG1 homologs from the black and yellow seeded B. rapa lines were used to transform an Arabidopsis ttg1 mutant and the results showed that the TTG1 homolog from the black seeded B. rapa recovered the Arabidopsis ttg1 mutant, while the yellow seeded homolog did not, suggesting that the deletion in the Brassica TTG1 homolog had led to the yellow seeded natural mutant. This was the first identified gene in Brassica species that simultaneously controlled both hairiness and seed coat color traits.

A genetic map was constructed with 353 sequence-related amplified polymorphism and 34 simple sequence repeat markers in oilseed rape (Brassica napus L.). The map consists of 19 linkage groups and covers 1,868 cM of the rapeseed genome. A recombinant doubled haploid (DH) population consisting of 150 lines segregating for oil content and other agronomic traits was produced using standard microspore culture techniques. The DH lines were phenotyped for days to flowering, oil content in the seed, and seed yield at three locations for 3 years, generating nine environments. Data from each of the environments were analyzed separately to detect quantitative trait loci (QTL) for these three phenotypic traits. For oil content, 27 QTL were identified on 14 linkage groups; individual QTL for oil content explained 4.20-30.20% of the total phenotypic variance. For seed yield, 18 QTL on 11 linkage groups were identified, and the phenotypic variance for seed yield, as explained by a single locus, ranged from 4.61 to 24.44%. Twenty-two QTL were also detected for days to flowering, and individual loci explained 4.41-48.28% of the total phenotypic variance.

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BackgroundSequence related amplified polymorphism (SRAP) is commonly used to construct high density genetic maps, map genes and QTL of important agronomic traits in crops and perform genetic diversity analysis without knowing sequence information. To combine next generation sequencing technology with SRAP, Illumina's Solexa sequencing was used to sequence tagged SRAP PCR products.ResultsThree sets of SRAP primers and three sets of tagging primers were used in 77,568 SRAP PCR reactions and the same number of tagging PCR reactions respectively to produce a pooled sample for Illumina's Solexa sequencing. After sequencing, 1.28 GB of sequence with over 13 million paired-end sequences was obtained and used to match Solexa sequences with their corresponding SRAP markers and to integrate Solexa sequences on an ultradense genetic map. The ultradense genetic bin map with 465 bins was constructed using a recombinant inbred (RI) line mapping population in B. rapa. For this ultradense genetic bin map, 9,177 SRAP markers, 1,737 integrated unique Solexa paired-end sequences and 46 SSR markers representing 10,960 independent genetic loci were assembled and 141 unique Solexa paired-end sequences were matched with their corresponding SRAP markers. The genetic map in B. rapa was aligned with the previous ultradense genetic map in B. napus through common SRAP markers in these two species. Additionally, SSR markers were used to perform alignment of the current genetic map with other five genetic maps in B. rapa and B. napus.ConclusionWe used SRAP to construct an ultradense genetic map with 10,960 independent genetic loci in B. rapa that is the most saturated genetic map ever constructed in this species. Using next generation sequencing, we integrated 1,878 Solexa sequences on the genetic map. These integrated sequences will be used to assemble the scaffolds in the B. rapa genome. Additionally, this genetic map may be used for gene cloning and marker development in B. rapa and B. napus.

Brassica rapa L. ssp. chinensis (L.) Hanelt, known as nonheading chinese cabbage in China, is an important vegetable in eastern Asia and its genetic improvement requires a genetic linkage map. The first genetic linkage map of nonheading chinese cabbage using 112 doubled haploid lines derived from a released F1 hybrid cultivar Shulü between two lines SW-3 and Su-124 was constructed in this paper. One hundred thirty-eight molecular markers were mapped into 14 linkage groups. Among these markers, there were 77 sequence-related amplified polymorphism markers, 27 simple sequence repeat markers, 21 random amplification polymorphic DNA markers, and 13 intersimple sequence repeat markers. Chi-square tests showed that 54 markers are distorted from Mendelian segregation ratios, and the direction of the distortion is mainly toward the maternal parent SW-3. The distortion affects not only the estimation of genetic distance, but also the order of distorted markers on a same linkage group. Given a specific marker order, the authors proposed a multipoint approach to correct the linkage map in an unbiased manner in an F2 population while considering distorted, dominant, and missing markers. A new method was used to correct the linkage map in the doubled haploid population mentioned earlier considering new, distorted, and missing markers. The total length of the corrected linkage map was 1923.75 cM, with an average marker spacing of 15.52 cM. The map will facilitate selective breeding and mapping of quantitative trait loci.

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Quantitative trait loci (QTLs) identified so far in Brassica were mainly generated in the final stage of plant development, which did not apply to the exploitation of genetic effects that were expressed during a specific developmental stage. Thus, the objective of this study was to simultaneously identify unconditional and conditional QTL associated with plant height at various stages of nonheading Chinese cabbage. One hundred twelve doubled haploid (DH) lines developed from the cross between nonheading Chinese cabbage lines ‘SW-13’ and ‘SU-124’ were used for QTL analysis of plant height by the composite interval mapping method combined with mixed genetic model. The map we used for QTL analysis was an updated version of the first genetic map of nonheading Chinese cabbage with 48 additional markers to the same DH population. With data from 2 years, a total of 11 unconditional QTLs in six linkage groups and 23 conditional QTLs in eight linkage groups were identified for plant height. The results indicated that the number and type of QTLs and their genetic effects for plant height were different in a series of measuring stages. Each QTL can explain 7.92% to 28.25% of the total phenotypic variation. Two QTLs (ph8-4 and ph8-5) were identified to be associated with plant height using both unconditional and conditional mapping methods simultaneously in 2 years. These results demonstrated that it is highly effective for mapping QTL of developmental traits using the unconditional and conditional analysis methodology.

A hybrid developed from a cross between two diverse Brassica napus cultivars ("Polo" and "Topas") was used to produce a microspore derived double haploid (DH) population and a single seed descent derived recombinant inbred (RI) population for genetic mapping. Each of the two populations consisting of 190 DH lines and 94 RI lines was characterized for various types (SSR, SRAP, ISSR, SCAR) of polymorphic molecular markers. The DH population was scored for 620 molecular markers while the RI population was scored for 349 molecular markers to construct two independent genetic maps. In both genetic maps, all of the molecular markers were found to cluster in 19 linkage groups (LGs) covered a total genome length of 2244.1 cM and 1649.1 cM for the DH and RI maps, respectively. The data from the two genetic maps was used to construct a consensus integrated genetic map covering a total genome length of 2464.9 cM. Previously published Brassica reference genetic maps were used to assign each of the nineteenLGs to corresponding Brassica napus chromosomes named N01 to N19. To our knowledge, this is the first integrated genetic map based on DH and RI populations developed from the same cross in Brassica napus.