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Identification of Genes Potentially Associated with the Fertility Instability of S-Type Cytoplasmic Male Sterility in Maize via Bulked Segregant RNA-Seq

View Article: PubMed Central - PubMed

ABSTRACT

S-type cytoplasmic male sterility (CMS-S) is the largest group among the three major types of CMS in maize. CMS-S exhibits fertility instability as a partial fertility restoration in a specific nuclear genetic background, which impedes its commercial application in hybrid breeding programs. The fertility instability phenomenon of CMS-S is controlled by several minor quantitative trait locus (QTLs), but not the major nuclear fertility restorer (Rf3). However, the gene mapping of these minor QTLs and the molecular mechanism of the genetic modifications are still unclear. Using completely sterile and partially rescued plants of fertility instable line (FIL)-B, we performed bulk segregant RNA-Seq and identified six potential associated genes in minor effect QTLs contributing to fertility instability. Analyses demonstrate that these potential associated genes may be involved in biological processes, such as floral organ differentiation and development regulation, energy metabolism and carbohydrates biosynthesis, which results in a partial anther exsertion and pollen fertility restoration in the partially rescued plants. The single nucleotide polymorphisms (SNPs) identified in two potential associated genes were validated to be related to the fertility restoration phenotype by KASP marker assays. This novel knowledge contributes to the understanding of the molecular mechanism of the partial fertility restoration of CMS-S in maize and thus helps to guide the breeding programs.

No MeSH data available.


Graphs of four KASP marker assays.KASP assays were developed for SNPs identified in two potential associated genes from RNA-Seq. Fertility instable line (FIL)-1 and FIL-2 were SNPs resided in GRMZM2G315401. FIL-3 and FIL-4 were SNPs detected in GRMZM2G430362. The triangles represent the recurrent parent of Jing724. Black data points are negative control and pink ones are ambiguous calling.
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pone.0163489.g006: Graphs of four KASP marker assays.KASP assays were developed for SNPs identified in two potential associated genes from RNA-Seq. Fertility instable line (FIL)-1 and FIL-2 were SNPs resided in GRMZM2G315401. FIL-3 and FIL-4 were SNPs detected in GRMZM2G430362. The triangles represent the recurrent parent of Jing724. Black data points are negative control and pink ones are ambiguous calling.

Mentions: To further assess the effect of the potential associated genes, SNPs identified in six potential associated genes were evaluated. Two SNPs in each of the GRMZM2G315401 and GRMZM2G430362 appeared to be conclusive, whose alleles and positions on B73 were included in Table 4. To further determine the correlation between these SNPs and the fertility phenotype, KASP marker assays were performed with 50 individuals of sterile plant and 50 partially rescued plants from the BC4 population. As expected, all the sterile individuals possessed the homozygous loci, and all the fertile plants exhibited heterozygous loci for all four SNPs with no exceptions (Table 4 and Fig 6). The PCR-based SNP assays validated the SNPs identified from RNA-Seq, further confirming the potential function of two associated genes in fertility instability.


Identification of Genes Potentially Associated with the Fertility Instability of S-Type Cytoplasmic Male Sterility in Maize via Bulked Segregant RNA-Seq
Graphs of four KASP marker assays.KASP assays were developed for SNPs identified in two potential associated genes from RNA-Seq. Fertility instable line (FIL)-1 and FIL-2 were SNPs resided in GRMZM2G315401. FIL-3 and FIL-4 were SNPs detected in GRMZM2G430362. The triangles represent the recurrent parent of Jing724. Black data points are negative control and pink ones are ambiguous calling.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5036866&req=5

pone.0163489.g006: Graphs of four KASP marker assays.KASP assays were developed for SNPs identified in two potential associated genes from RNA-Seq. Fertility instable line (FIL)-1 and FIL-2 were SNPs resided in GRMZM2G315401. FIL-3 and FIL-4 were SNPs detected in GRMZM2G430362. The triangles represent the recurrent parent of Jing724. Black data points are negative control and pink ones are ambiguous calling.
Mentions: To further assess the effect of the potential associated genes, SNPs identified in six potential associated genes were evaluated. Two SNPs in each of the GRMZM2G315401 and GRMZM2G430362 appeared to be conclusive, whose alleles and positions on B73 were included in Table 4. To further determine the correlation between these SNPs and the fertility phenotype, KASP marker assays were performed with 50 individuals of sterile plant and 50 partially rescued plants from the BC4 population. As expected, all the sterile individuals possessed the homozygous loci, and all the fertile plants exhibited heterozygous loci for all four SNPs with no exceptions (Table 4 and Fig 6). The PCR-based SNP assays validated the SNPs identified from RNA-Seq, further confirming the potential function of two associated genes in fertility instability.

View Article: PubMed Central - PubMed

ABSTRACT

S-type cytoplasmic male sterility (CMS-S) is the largest group among the three major types of CMS in maize. CMS-S exhibits fertility instability as a partial fertility restoration in a specific nuclear genetic background, which impedes its commercial application in hybrid breeding programs. The fertility instability phenomenon of CMS-S is controlled by several minor quantitative trait locus (QTLs), but not the major nuclear fertility restorer (Rf3). However, the gene mapping of these minor QTLs and the molecular mechanism of the genetic modifications are still unclear. Using completely sterile and partially rescued plants of fertility instable line (FIL)-B, we performed bulk segregant RNA-Seq and identified six potential associated genes in minor effect QTLs contributing to fertility instability. Analyses demonstrate that these potential associated genes may be involved in biological processes, such as floral organ differentiation and development regulation, energy metabolism and carbohydrates biosynthesis, which results in a partial anther exsertion and pollen fertility restoration in the partially rescued plants. The single nucleotide polymorphisms (SNPs) identified in two potential associated genes were validated to be related to the fertility restoration phenotype by KASP marker assays. This novel knowledge contributes to the understanding of the molecular mechanism of the partial fertility restoration of CMS-S in maize and thus helps to guide the breeding programs.

No MeSH data available.