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Genetic localization of the SPC gene controlling pod coiling direction in Medicago truncatula

Xiaocheng Yu, Qiulin Qin, Xia Wu, Dandan Li, Shengming Yang
Genes & genomics 2020 v.42 no.7 pp. 735-742
Medicago truncatula, computer software, databases, genes, genetic analysis, legumes, loci, models, nucleotide sequences, pods, protein-serine-threonine kinases, quantitative polymerase chain reaction, reverse transcriptase polymerase chain reaction, sequence analysis, single nucleotide polymorphism, vacuoles
BACKGROUND: Handedness in plants introduced by helical growth of organs is frequently observed, and it has fascinated plant scientists for decades. However, the genetic control of natural handedness has not been revealed. In the model legume Medicago truncatula, pods can be coiled in a clockwise or anti-clockwise manner, providing a model for genetic analysis of plant handedness. OBJECTIVE: We aimed to localize the Sense of Pod Coiling (SPC) gene controlling pod coiling direction in M. truncatula. METHODS: Linkage analysis was used with a biparental population for fine mapping of the SPC gene. The genome sequence of M. truncatula Mt4.0 was used for marker identification and physical mapping. Single nucleotide polymorphisms (SNPs) between the parental lines were converted to CAPS (cleaved amplified polymorphic sequences) markers. Genetic map was constructed using the software JoinMap version 3.0. Gene predication and annotation provided by the M. truncatula genome database (http://www.medicagogenome.org) was confirmed with the programs of FGENESH and Pfam 32.0, respectively. Quantitative reverse transcription PCR (qRT-PCR) was used to analyze the relative expression levels of candidate genes. RESULTS: The genetic analysis indicated that the anti-clockwise coiling is dominant to clockwise and is controlled by the single gene, SPC. The SPC gene was delimited to a 250 kb-region on Chromosome 7. Total of 15 protein-coding genes were identified in the SPC locus through gene annotation and sequence analysis. Of those, two genes, potentially encoding a receptor-like kinase and a vacuolar cation/proton exchanger respectively, were selected as candidates for the SPC gene. CONCLUSIONS: The result presented here lay a foundation for gene cloning of SPC, which will help us to understand the molecular mechanisms underlying helical growth in plant organs.