Verification And Transcriptome Analysis Of A Minor QTL QSC3.1 For Seed Coat Color In Brassica Rapa

Brasssica rapa is an important vegetable,oil and feed crop,which is widely cultivated worldwide.Yellow seeds,as high quality oil extracting materials,have advantages of high oil content and high protein content.In this study,the recombinant inbred line(RIL)population and chromosome segment substitution line(CSSL)population were constructed between the yellow-seeded B.rapa Rc Br(P2)and the dark brown-seed Chinese cabbage 08A061.The RIL and CSSL population were used for QTL identification and validation of the seed coat color of B.rapa.The candidate genes controlling seed coat color of B.rapa in confidence interval on Chr.A03 were predicted by transcriptome sequencing analysis.The results are as follows:1.In RIL population,nine color-related QTLs were detected by visual and chromameter methods.Four were detected by visual and five were detected by chromameter,respectively.These QTLs were located on chromosomes A03,A06,A08 and A09 respectively.Two major QTLs with the same location were identified on chromosome A09,and the other seven were minor ones.2.The CSSL population which harbored the candidate interval for seed coat color was selected to validate the identified QTLs in RIL population.In two different environments,the phenotypes of CSSL-38 and CSSL-111 were significantly different from those of yellow-seeded parents.Two co-localized major QTLs,q SC9.1 and q SCb9.1,and one minor QTL,q SC3.1,identified in the RILs were successfully validated by selecting the corresponding NILs in the CSSLs.3.The seeds of brown-seeded NIL(CSSL-38)and yellow-seeded parent Rc Br(P2)were selected for transcriptome sequencing at two developmental stages,14 days and 21 days after pollinating.We speculate that a regulatory gene Bra A03g043570.3C(TT16),two structural genes Bra A03g039680.3C(4CL)and Bra A03g045540.3C(F3H)are candidate genes for controlling seed coat color in B.rapa bwteen the candidate interval of Chr.A03 by identifying the differentially expressed genes(DEGs),functional enrichment analysis of GO and KEGG pathway of DEGs and gene functional annotation.