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Identification of a novel marker and its associated laccase gene for regulating ear length in tropical and subtropical maize lines

Maize ear length has garnered considerable attention due to its high correlation with yield. In this study, six maize inbred lines of significant importance in maize breeding were used as parents. The temperate maize inbred line Ye107, characterized by a short ear, was crossed with five tropical or subtropical inbred lines featuring longer ears, creating a multi-parent population displaying significant variations in ear length. Through genome-wide association studies and mutation analysis, the A/G variation at SNP_183573532 on chromosome 3 was identified as an effective site for discriminating long-ear maize. Furthermore, the associated gene Zm00001d042906 was found to correlate with maize ear length.

Yaqi BiFuyan JiangYudong ZhangZiwei LiTianhui KuangRanjan K. ShawMuhammad AdnanKunzhi Li & Xingming Fan

Theoretical and Applied Genetics; April 2024; vol. 137; article 94

Key message

This study revealed the identification of a novel gene, Zm00001d042906, that regulates maize ear length by modulating lignin synthesis and reported a molecular marker for selecting maize lines with elongated ears.

Abstract

Maize ear length has garnered considerable attention due to its high correlation with yield. In this study, six maize inbred lines of significant importance in maize breeding were used as parents. The temperate maize inbred line Ye107, characterized by a short ear, was crossed with five tropical or subtropical inbred lines featuring longer ears, creating a multi-parent population displaying significant variations in ear length. Through genome-wide association studies and mutation analysis, the A/G variation at SNP_183573532 on chromosome 3 was identified as an effective site for discriminating long-ear maize. Furthermore, the associated gene Zm00001d042906 was found to correlate with maize ear length. Zm00001d042906 was functionally annotated as a laccase (Lac4), which showed activity and influenced lignin synthesis in the midsection cells of the cob, thereby regulating maize ear length. This study further reports a novel molecular marker and a new gene that can assist maize breeding programs in selecting varieties with elongated ears.

 

See https://link.springer.com/article/10.1007/s00122-024-04587-z

 

Figure 2: Analysis of phenotypic and genotypic data. a Frequency distributions of EL of the MPP at three locations. b Principal component analysis of MPP. Red, orange, purple, blue and green dots represent the families of RIL_CML312, RIL_TML418, RIL_TRL02, RIL_CML373 and RIL_YML226, respectively. c GWAS results of the MPP at three locations. d Significant differences in EL between two haplotypes (AA, GG) at three locations, with ***indicating P < 0.0001. e The proportions of the two haplotypes observed in five RIL subpopulations. f Maize hybrid Yunrui88 resulting from the cross TRL02 × Ye107. g Hybrid Xingdan106 obtained from the cross TML418 × Ye107 and h the linkage between genes Zm00001d042905 and Zm00001d042906 (colour figure online).

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