Dataset Information

Development of the PARMS Marker of the Dominant Genic Male Sterility (DGMS) Line and Its Utilization in Rapeseed (Brassica napus L.) Breeding.

ABSTRACT: The 8029AB line is a dominant genic male sterility (DGMS) two-type line in Brassica napus L., which can be used in a three-line approach for the seed production of rapeseed hybrids. Genetic analyses have demonstrated that the sterility of 8029A is controlled by a single dominant nuclear gene (BnMS5e) interacting with one recessive gene (BnMS5c). Six pairs of penta-primer amplification refractory mutation system (PARMS) markers were designed according to the sequence of BnMS5a, BnMS5c and BnMS5e. Two pairs of these PARMS markers were successfully identified and validated. The PARMS markers MS5-1Fc/MS5-1Ft/MS5-1R12 could distinguish BnMS5c from BnMS5a/BnMS5e, and the PARMS markers MS5-2Ft/MS5-2Fa/MS5-1R12 could genotype BnMS5a and BnMS5c/BnMS5e. The combination of these two pairs of PARMS markers could be used to identify the presence or absence of BnMS5a/BnMS5c/BnMS5e effectively. Consequently, marker-assisted selection can be carried out in the early generation to shorten the breeding period and improve the breeding efficiency.

SUBMITTER: Li Z

PROVIDER: S-EPMC8840721 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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Development of the PARMS Marker of the Dominant Genic Male Sterility (DGMS) Line and Its Utilization in Rapeseed (Brassica napus L.) Breeding.

Li Zhen Z Yuan Rong R Wang Miao M Hong Meiyan M Zhu Li L Li Xiaofei X Guo Ruixing R Wu Gang G Zeng Xinhua X

Plants (Basel, Switzerland) 20220203 3

The 8029AB line is a dominant genic male sterility (DGMS) two-type line in Brassica napus L., which can be used in a three-line approach for the seed production of rapeseed hybrids. Genetic analyses have demonstrated that the sterility of 8029A is controlled by a single dominant nuclear gene (BnMS5e) interacting with one recessive gene (BnMS5c). Six pairs of penta-primer amplification refractory mutation system (PARMS) markers were designed according to ...[more]

PMID: 35161402

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Project description:Rapeseed is the third leading source of edible oil in the world. Genic male sterility (GMS) lines provide crucial material for harnessing heterosis for rapeseed. GMS lines have been widely used successfully for rapeseed hybrid production. The physiological and molecular mechanism of pollen development in GMS lines of rapeseed (Brassica napus L.) need to be determined for the creation of hybrids and cultivation of new varieties. However, limited studies have focused on systematically mining genes that regulate the pollen development of GMS lines in B. napus. In the present study, to determine the stage at which pollen development begins to show abnormality in the GMS lines, we performed semi-thin section analysis of the anthers with five pollen development stages. The results indicated that the abnormal pollen development in DGMS lines might start at the meiotic stage, and abnormal pollen development in RGMS lines probably occurred before the tetrad stage. To investigate the critical genes and pathways involved in pollen development in GMS lines, we constructed and sequenced 24 transcriptome libraries for the flower buds from the fertile and sterile lines of two recessive GMS (RGMS) lines (6251AB and 6284AB) and two dominant GMS (DGMS) lines (4001AB and 4006AB). A total of 23,554 redundant DEGs with over two-fold change between sterile and fertile lines were obtained. A total of 346 DEGs were specifically related to DGMS, while 1,553 DEGs were specifically related to RGMS. A total of 1,545 DEGs were shared between DGMS and RGMS. And 253 transcription factors were found to be differentially expressed between the sterile and fertile lines of GMS. In addition, 6,099 DEGs possibly related to anther, pollen, and microspore development processes were identified. Many of these genes have been reported to be involved in anther and microspore developmental processes. Several DEGs were speculated to be key genes involved in the regulation of fertility. Three differentially expressed genes were randomly selected and their expression levels were verified by quantitative PCR (qRT-PCR). The results of qRT-PCR largely agreed with the transcriptome sequencing results. Our findings provide a global view of genes that are potentially involved in GMS occurrence. The expression profiles and function analysis of these DEGs were provided to expand our understanding of the complex molecular mechanism in pollen and sterility development in B. napus.

Project description:BackgroundBrassica napus is the third leading source of edible oil in the world. Genic male sterility (GMS) lines provide crucial material for harnessing heterosis for rapeseed. GMS lines have been used successfully for rapeseed hybrid production in China. MicroRNAs (miRNAs) play crucial regulatory roles in various plant growth, development, and stress response processes. However, reports on miRNAs that regulate the pollen development of GMS lines in B. napus are few.ResultsIn this study, 12 small RNA and transcriptome libraries were constructed and sequenced for the flower buds from the fertile and sterile lines of two recessive GMS (RGMS) lines, namely, "6251AB" and "6284AB". At the same time, 12 small RNA and transcriptome libraries were also constructed and sequenced for the flower buds from the fertile and sterile lines of two dominant GMS (DGMS) lines, namely, "4001AB" and "4006AB". Based on the results, 46 known miRNAs, 27 novel miRNAs on the other arm of known pre-miRNAs, and 44 new conserved miRNAs were identified. Thirty-five pairs of novel miRNA-3p/miRNA-5p were found. Among all the identified miRNAs, fifteen differentially expressed miRNAs with over 1.5-fold change between flower buds of sterile and fertile lines were identified, including six differentially expressed miRNAs between "4001A" and "4001B", two differentially expressed miRNAs between "4006A" and "4006B", four differentially expressed miRNAs between "6251A" and "6251B", and ten differentially expressed miRNAs between "6284A" and "6284B". The correlation analysis of small RNA and transcriptome sequencing was conducted. And 257 candidate target genes were predicted for the 15 differentially expressed miRNAs. The results of 5' modified RACE indicated that BnaA09g48720D, BnaA09g11120D, and BnaCnng51960D were cleaved by bna-miR398a-3p, bna-miR158-3p and bna-miR159a, respectively. Among the differentially expressed miRNAs, miR159 was chosen to analyze its function. Overexpression of bna-miR159 in Arabidopsis resulted in decreased seed setting rate, and shortened siliques, illustrating that miR159 may regulate the fertility and silique development in rapeseed.ConclusionsOur findings provide an overview of miRNAs that are potentially involved in GMS and pollen development. New information on miRNAs and their related target genes are provided to exploit the GMS mechanism and reveal the miRNA networks in B. napus.

Project description:Background Studying the relationships between rapeseed seed yield (SY) and its yield-related traits can assist rapeseed breeders in the efficient indirect selection of high-yielding varieties. However, since the conventional and linear methods cannot interpret the complicated relations between SY and other traits, employing advanced machine learning algorithms is inevitable. Our main goal was to find the best combination of machine learning algorithms and feature selection methods to maximize the efficiency of indirect selection for rapeseed SY. Results To achieve that, twenty-five regression-based machine learning algorithms and six feature selection methods were employed. SY and yield-related data from twenty rapeseed genotypes were collected from field experiments over a period of 2 years (2019–2021). Root mean square error (RMSE), mean absolute error (MAE), and determination coefficient (R2) were used to evaluate the performance of the algorithms. The best performance with all fifteen measured traits as inputs was achieved by the Nu-support vector regression algorithm with quadratic polynomial kernel function (R2 = 0.860, RMSE = 0.266, MAE = 0.210). The multilayer perceptron neural network algorithm with identity activation function (MLPNN-Identity) using three traits obtained from stepwise and backward selection methods appeared to be the most efficient combination of algorithms and feature selection methods (R2 = 0.843, RMSE = 0.283, MAE = 0.224). Feature selection suggested that the set of pods per plant and days to physiological maturity along with plant height or first pod height from the ground are the most influential traits in predicting rapeseed SY. Conclusion The results of this study showed that MLPNN-Identity along with stepwise and backward selection methods can provide a robust combination to accurately predict the SY using fewer traits and therefore help optimize and accelerate SY breeding programs of rapeseed. Supplementary Information The online version contains supplementary material available at 10.1186/s13007-023-01035-9.

Dataset Information

Development of the PARMS Marker of the Dominant Genic Male Sterility (DGMS) Line and Its Utilization in Rapeseed (Brassica napus L.) Breeding.

Publications

Development of the PARMS Marker of the Dominant Genic Male Sterility (DGMS) Line and Its Utilization in Rapeseed (<i>Brassica napus</i> L.) Breeding.

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