Identification of Genomic Regions Associated with Multi-silique Trait in Brassica Napus

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2019 Apr 25

PMID 31014236

Citations 6

Authors

Liang Chai

Jinfang Zhang

Kun Lu

Haojie Li

Lintao Wu

Hongshen Wan

Benchuan Zheng

Cheng Cui

Jun Jiang

Liangcai Jiang

Affiliations

Soon will be listed here.

Abstract

Background: Although rapeseed (Brassica napus L.) mutant forming multiple siliques was morphologically described and considered to increase the silique number per plant, an important agronomic trait in this crop, the molecular mechanism underlying this beneficial trait remains unclear. Here, we combined bulked-segregant analysis (BSA) and whole genome re-sequencing (WGR) to map the genomic regions responsible for the multi-silique trait using two pools of DNA from the near-isogenic lines (NILs) zws-ms (multi-silique) and zws-217 (single-silique). We used the Euclidean Distance (ED) to identify genomic regions associated with this trait based on both SNPs and InDels. We also conducted transcriptome sequencing to identify differentially expressed genes (DEGs) between zws-ms and zws-217.

Results: Genetic analysis using the ED algorithm identified three SNP- and two InDel-associated regions for the multi-silique trait. Two highly overlapped parts of the SNP- and InDel-associated regions were identified as important intersecting regions, which are located on chromosomes A09 and C08, respectively, including 2044 genes in 10.20-MB length totally. Transcriptome sequencing revealed 129 DEGs between zws-ms and zws-217 in buds, including 39 DEGs located in the two abovementioned associated regions. We identified candidate genes involved in multi-silique formation in rapeseed based on the results of functional annotation.

Conclusions: This study identified the genomic regions and candidate genes related to the multi-silique trait in rapeseed.

Citing Articles

Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs.

Dwivedi S, Quiroz L, Reddy A, Spillane C, Ortiz R Int J Mol Sci. 2023; 24(20).

PMID: 37894886 PMC: 10607462. DOI: 10.3390/ijms242015205.

Analysis of Altered Flowering Related Genes in a Multi-Silique Rapeseed ( L.) Line zws-ms Based on Combination of Genome, Transcriptome and Proteome Data.

Chai L, Li H, Zhao X, Cui C, Zheng B, Zhang K Plants (Basel). 2023; 12(13).

PMID: 37446989 PMC: 10346454. DOI: 10.3390/plants12132429.

Evaluation of the Possible Contribution of Various Regulatory Genes to Determination of Carpel Number as a Potential Mechanism for Optimal Agricultural Yield.

Abiri N, Sinjushin A, Tekdal D, Cetiner S Int J Mol Sci. 2022; 23(17).

PMID: 36077121 PMC: 9456115. DOI: 10.3390/ijms23179723.

Investigation of Thermomorphogenesis-Related Genes for a Multi-Silique Trait in by Comparative Transcriptome Analysis.

Chai L, Zhang J, Li H, Cui C, Jiang J, Zheng B Front Genet. 2021; 12:678804.

PMID: 34367242 PMC: 8343136. DOI: 10.3389/fgene.2021.678804.

Fine mapping and molecular marker development of the Fs gene controlling fruit spines in spinach (Spinacia oleracea L.).

Liu Z, Lu T, Feng C, Zhang H, Xu Z, Correll J Theor Appl Genet. 2021; 134(5):1319-1328.

PMID: 33515081 DOI: 10.1007/s00122-021-03772-8.

References

Palmer R, Horner H . Genetics and cytology of a genic male-sterile, female-sterile mutant from a transposon-containing soybean population. J Hered. 2000; 91(5):378-83. DOI: 10.1093/jhered/91.5.378. View

Mouradov A, Cremer F, Coupland G . Control of flowering time: interacting pathways as a basis for diversity. Plant Cell. 2002; 14 Suppl:S111-30. PMC: 151251. DOI: 10.1105/tpc.001362. View

Komeda Y . Genetic regulation of time to flower in Arabidopsis thaliana. Annu Rev Plant Biol. 2004; 55:521-35. DOI: 10.1146/annurev.arplant.55.031903.141644. View

Jenik P, Jurkuta R, Barton M . Interactions between the cell cycle and embryonic patterning in Arabidopsis uncovered by a mutation in DNA polymerase epsilon. Plant Cell. 2005; 17(12):3362-77. PMC: 1315375. DOI: 10.1105/tpc.105.036889. View

Berg M, Rogers R, Muralla R, Meinke D . Requirement of aminoacyl-tRNA synthetases for gametogenesis and embryo development in Arabidopsis. Plant J. 2005; 44(5):866-78. DOI: 10.1111/j.1365-313X.2005.02580.x. View

Mo P, Zhu Y, Liu X, Zhang A, Yan C, Wang D . Identification of two phosphatidylinositol/phosphatidylcholine transfer protein genes that are predominately transcribed in the flowers of Arabidopsis thaliana. J Plant Physiol. 2006; 164(4):478-86. DOI: 10.1016/j.jplph.2006.03.014. View

Michelmore R, Paran I, Kesseli R . Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci U S A. 1991; 88(21):9828-32. PMC: 52814. DOI: 10.1073/pnas.88.21.9828. View

Hanania U, Velcheva M, Or E, Flaishman M, Sahar N, Perl A . Silencing of chaperonin 21, that was differentially expressed in inflorescence of seedless and seeded grapes, promoted seed abortion in tobacco and tomato fruits. Transgenic Res. 2006; 16(4):515-25. DOI: 10.1007/s11248-006-9044-0. View

Palmer R, Sandhu D, Curran K, Bhattacharyya M . Molecular mapping of 36 soybean male-sterile, female-sterile mutants. Theor Appl Genet. 2008; 117(5):711-9. DOI: 10.1007/s00122-008-0812-5. View

10.

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

11.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

12.

Varshney R, Nayak S, May G, Jackson S . Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol. 2009; 27(9):522-30. DOI: 10.1016/j.tibtech.2009.05.006. View

13.

Wang L, Feng Z, Wang X, Wang X, Zhang X . DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics. 2009; 26(1):136-8. DOI: 10.1093/bioinformatics/btp612. View

14.

Zhao D . Control of anther cell differentiation: a teamwork of receptor-like kinases. Sex Plant Reprod. 2009; 22(4):221-8. DOI: 10.1007/s00497-009-0106-3. View

15.

Castonguay Y, Cloutier J, Bertrand A, Michaud R, Laberge S . SRAP polymorphisms associated with superior freezing tolerance in alfalfa (Medicago sativa spp. sativa). Theor Appl Genet. 2010; 120(8):1611-9. DOI: 10.1007/s00122-010-1280-2. View

16.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A . The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20(9):1297-303. PMC: 2928508. DOI: 10.1101/gr.107524.110. View

17.

Yang Z, Peng Z, Wei S, Yu Y, Cai P . Identification of differentially expressed genes in three-pistil mutation in wheat using annealing control primer system. Gene. 2011; 485(2):81-4. DOI: 10.1016/j.gene.2011.06.009. View

18.

Huang H, Jiang W, Hu Y, Wu P, Zhu J, Liang W . BR signal influences Arabidopsis ovule and seed number through regulating related genes expression by BZR1. Mol Plant. 2012; 6(2):456-69. DOI: 10.1093/mp/sss070. View

19.

Sprunck S, Rademacher S, Vogler F, Gheyselinck J, Grossniklaus U, Dresselhaus T . Egg cell-secreted EC1 triggers sperm cell activation during double fertilization. Science. 2012; 338(6110):1093-7. DOI: 10.1126/science.1223944. View

20.

Hill J, Demarest B, Bisgrove B, Gorsi B, Su Y, Yost H . MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq. Genome Res. 2013; 23(4):687-97. PMC: 3613585. DOI: 10.1101/gr.146936.112. View