Mean yield, IPCA1, IPCA2, ASVi and ASVi rank for genotypes over three locations.

Mean yield, IPCA1, IPCA2, ASVi and ASVi rank for genotypes over three locations.</p

Monomorphic restriction site present in both AI 535 and AI 536 at 440 bp (1161) around the 1311nucleotide position (inclusive) in the <i>fea</i>2 gene.

Monomorphic restriction site present in both AI 535 and AI 536 at 440 bp (1161) around the 1311nucleotide position (inclusive) in the fea2 gene.</p

Identification of SNPs in <i>fea</i>2 gene between high and low KRN genotypes.

Identification of SNPs in fea2 gene between high and low KRN genotypes.</p

Pedigree of inbred lines used in this study.

BackgroundKernel row number (KRN) is an important yield component trait with a direct impact on the productivity of maize. The variability in KRN is influenced by the inflorescence meristem size, which is determined by the CLAVATA-WUSCHEL pathway. A CLAVATA receptor-like protein, encoded by the FASCIATED EAR2 (fea2gene), enhances the growth of inflorescence meristem and is thus involved in the determination of KRN. The amplicon sequencing-based method was employed to dissect the allelic variation of the fea2 gene in tropical field corn.Methodology/Principal findingAmplicon-based sequencing of AI 535 (Low KRN) and AI 536 (High KRN) was undertaken for the gene fea 2 gene that codes for KRN in maize. Upon multiple sequence alignment of both sequences, A to T transversion at the 1311 position was noticed between Low KRN and High KRN genotypes resulting in different allelic forms of a fea2 gene in tropical maize. An allele-specific primer 1311 fea2.1 was designed and validated that can differentiate High and Low KRN genotypes.Conclusion/SignificanceMaize has high variability for KRN and is exemplified by the wide values ranging from 8–26 KRN in the maize germpalsm. The sequence-based approach of SNP detection through the use of a specific primer facilitated the detection of variation present in the target trait. This makes it possible to capture these variations in the early generation. In the study, the PCR-based differentiation method described for the identification of desirable high KRN genotypes would augment the breeding programs for improving the productivity of field corn.</div

Fig 2 -

(a) Comparative nucleotide sequence of test and reference genotypes showing transversion (A: T) at 1311bp of fea2 gene, (b) Comparative amino acid sequence of test and reference genotypes showing conversion of cysteine/serine due to A: T transversion.</p

Mean and range for KRN trait of selected genotypes across environments.

Mean and range for KRN trait of selected genotypes across environments.</p

Contrasting parents for high and low KRN trait.

BackgroundKernel row number (KRN) is an important yield component trait with a direct impact on the productivity of maize. The variability in KRN is influenced by the inflorescence meristem size, which is determined by the CLAVATA-WUSCHEL pathway. A CLAVATA receptor-like protein, encoded by the FASCIATED EAR2 (fea2gene), enhances the growth of inflorescence meristem and is thus involved in the determination of KRN. The amplicon sequencing-based method was employed to dissect the allelic variation of the fea2 gene in tropical field corn.Methodology/Principal findingAmplicon-based sequencing of AI 535 (Low KRN) and AI 536 (High KRN) was undertaken for the gene fea 2 gene that codes for KRN in maize. Upon multiple sequence alignment of both sequences, A to T transversion at the 1311 position was noticed between Low KRN and High KRN genotypes resulting in different allelic forms of a fea2 gene in tropical maize. An allele-specific primer 1311 fea2.1 was designed and validated that can differentiate High and Low KRN genotypes.Conclusion/SignificanceMaize has high variability for KRN and is exemplified by the wide values ranging from 8–26 KRN in the maize germpalsm. The sequence-based approach of SNP detection through the use of a specific primer facilitated the detection of variation present in the target trait. This makes it possible to capture these variations in the early generation. In the study, the PCR-based differentiation method described for the identification of desirable high KRN genotypes would augment the breeding programs for improving the productivity of field corn.</div

Validation of novel primer 1311fea2.1 in 155 F₂ progenies.

Validation of novel primer 1311fea2.1 in 155 F2 progenies.</p

Allele-specific amplification of 1311fea2.1 in high and low KRN genotypes (AI 535 and AI 505: Low KRN, AI 536 and AI 542: High KRN, L: 50bp ladder).

(a) Introduce the mismatch. (b) L-Ladder: 50bp, AI-535 low KRN inbreds (Not amplified), AI 536 & AI 542: High KRN inbred amplified.</p

Ramachandran plot and proposed model for <i>fea2</i> gene for high (AI 536) and Low (AI 535) KRN trait.

(a) & (b) Ramchandran plot and proposed protein model of feq2 gene with a sequence identity fo 29.94% with template LRR receptor-like serine/threonine-protein kinase for Low KRN (AI 535), (c) & (d) Ramchandran plot and proposed protein model of fea2 gene with a sequence identity of 30.53% with template LRR receptor-like serine/threonine-protein kinase for Low KRN (AI 536).</p