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Genetic dissection of seed oil and protein content and identification of networks associated with oil content in Brassica napus

View Article: PubMed Central - PubMed

ABSTRACT

High-density linkage maps can improve the precision of QTL localization. A high-density SNP-based linkage map containing 3207 markers covering 3072.7 cM of the Brassica napus genome was constructed in the KenC-8 × N53-2 (KNDH) population. A total of 67 and 38 QTLs for seed oil and protein content were identified with an average confidence interval of 5.26 and 4.38 cM, which could explain up to 22.24% and 27.48% of the phenotypic variation, respectively. Thirty-eight associated genomic regions from BSA overlapped with and/or narrowed the SOC-QTLs, further confirming the QTL mapping results based on the high-density linkage map. Potential candidates related to acyl-lipid and seed storage underlying SOC and SPC, respectively, were identified and analyzed, among which six were checked and showed expression differences between the two parents during different embryonic developmental periods. A large primary carbohydrate pathway based on potential candidates underlying SOC- and SPC-QTLs, and interaction networks based on potential candidates underlying SOC-QTLs, was constructed to dissect the complex mechanism based on metabolic and gene regulatory features, respectively. Accurate QTL mapping and potential candidates identified based on high-density linkage map and BSA analyses provide new insights into the complex genetic mechanism of oil and protein accumulation in the seeds of rapeseed.

No MeSH data available.


KN high-density genetic linkage map, distribution of markers, identified QTLs, consensus QTLs of SOC and SPC on each linkage group, and colinearity of the linkage map and B. napus reference genome.The blocks with green bands at the outermost circle represent the 19 genetic linkage groups and the marker distribution. The third circle (from the outermost one) represents the 19 chromosomes of B. napus. The lines connecting them represent their col-linearity relationship. The 12 inner circles with 3 colors represent 12 microenvironments in winter-type, spring-type and semi winter-type rapeseed growing areas, respectively. The short bars with a red and blue color within the 12 inner circles represent QTLs identified in different environments and linkage groups, and they are located between the outermost two circles representing consensus QTLs.
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f1: KN high-density genetic linkage map, distribution of markers, identified QTLs, consensus QTLs of SOC and SPC on each linkage group, and colinearity of the linkage map and B. napus reference genome.The blocks with green bands at the outermost circle represent the 19 genetic linkage groups and the marker distribution. The third circle (from the outermost one) represents the 19 chromosomes of B. napus. The lines connecting them represent their col-linearity relationship. The 12 inner circles with 3 colors represent 12 microenvironments in winter-type, spring-type and semi winter-type rapeseed growing areas, respectively. The short bars with a red and blue color within the 12 inner circles represent QTLs identified in different environments and linkage groups, and they are located between the outermost two circles representing consensus QTLs.

Mentions: Of the 52157 SNP probes on the Brassica 60 K array, approximately 34.72% were polymorphic between the two parents and displayed segregation within the KNDH population. Finally, 18109 polymorphic SNPs were grouped into 3764 SNP-bins. All 3764 SNP-bins merged with 495 non-SNP markers (SSR and STS) were used for linkage map construction. A set of 3207 markers including 3106 SNP-bins and 101 non-SNPs were successfully assigned to 19 linkage groups (Table 1). The integrated map had a total length of 3072.7 cM with an average distance of 0.96 cM between adjacent markers (covering 1398.6 cM and 1674.1 cM for the A and C genomes, respectively). The number of loci in the 19 linkage groups ranged from 77 (A08) to 324 (A03), and the length ranged from 80.1 (A05) to 337.1 cM (C03), with a mean value of 161.72 cM (Table 1, and Fig. 1). The marker density of the 19 linkage groups varied; the highest marker density was on chromosome A04, with 156 markers distributed over a genetic map distance of 86.8 cM.


Genetic dissection of seed oil and protein content and identification of networks associated with oil content in Brassica napus
KN high-density genetic linkage map, distribution of markers, identified QTLs, consensus QTLs of SOC and SPC on each linkage group, and colinearity of the linkage map and B. napus reference genome.The blocks with green bands at the outermost circle represent the 19 genetic linkage groups and the marker distribution. The third circle (from the outermost one) represents the 19 chromosomes of B. napus. The lines connecting them represent their col-linearity relationship. The 12 inner circles with 3 colors represent 12 microenvironments in winter-type, spring-type and semi winter-type rapeseed growing areas, respectively. The short bars with a red and blue color within the 12 inner circles represent QTLs identified in different environments and linkage groups, and they are located between the outermost two circles representing consensus QTLs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5385559&req=5

f1: KN high-density genetic linkage map, distribution of markers, identified QTLs, consensus QTLs of SOC and SPC on each linkage group, and colinearity of the linkage map and B. napus reference genome.The blocks with green bands at the outermost circle represent the 19 genetic linkage groups and the marker distribution. The third circle (from the outermost one) represents the 19 chromosomes of B. napus. The lines connecting them represent their col-linearity relationship. The 12 inner circles with 3 colors represent 12 microenvironments in winter-type, spring-type and semi winter-type rapeseed growing areas, respectively. The short bars with a red and blue color within the 12 inner circles represent QTLs identified in different environments and linkage groups, and they are located between the outermost two circles representing consensus QTLs.
Mentions: Of the 52157 SNP probes on the Brassica 60 K array, approximately 34.72% were polymorphic between the two parents and displayed segregation within the KNDH population. Finally, 18109 polymorphic SNPs were grouped into 3764 SNP-bins. All 3764 SNP-bins merged with 495 non-SNP markers (SSR and STS) were used for linkage map construction. A set of 3207 markers including 3106 SNP-bins and 101 non-SNPs were successfully assigned to 19 linkage groups (Table 1). The integrated map had a total length of 3072.7 cM with an average distance of 0.96 cM between adjacent markers (covering 1398.6 cM and 1674.1 cM for the A and C genomes, respectively). The number of loci in the 19 linkage groups ranged from 77 (A08) to 324 (A03), and the length ranged from 80.1 (A05) to 337.1 cM (C03), with a mean value of 161.72 cM (Table 1, and Fig. 1). The marker density of the 19 linkage groups varied; the highest marker density was on chromosome A04, with 156 markers distributed over a genetic map distance of 86.8 cM.

View Article: PubMed Central - PubMed

ABSTRACT

High-density linkage maps can improve the precision of QTL localization. A high-density SNP-based linkage map containing 3207 markers covering 3072.7 cM of the Brassica napus genome was constructed in the KenC-8 × N53-2 (KNDH) population. A total of 67 and 38 QTLs for seed oil and protein content were identified with an average confidence interval of 5.26 and 4.38 cM, which could explain up to 22.24% and 27.48% of the phenotypic variation, respectively. Thirty-eight associated genomic regions from BSA overlapped with and/or narrowed the SOC-QTLs, further confirming the QTL mapping results based on the high-density linkage map. Potential candidates related to acyl-lipid and seed storage underlying SOC and SPC, respectively, were identified and analyzed, among which six were checked and showed expression differences between the two parents during different embryonic developmental periods. A large primary carbohydrate pathway based on potential candidates underlying SOC- and SPC-QTLs, and interaction networks based on potential candidates underlying SOC-QTLs, was constructed to dissect the complex mechanism based on metabolic and gene regulatory features, respectively. Accurate QTL mapping and potential candidates identified based on high-density linkage map and BSA analyses provide new insights into the complex genetic mechanism of oil and protein accumulation in the seeds of rapeseed.

No MeSH data available.