Genome‐wide identification of candidate phosphate starvation responsive genes and the development of intron length polymorphism markers in maize

Abstract

To develop genetic markers associated with tolerance to low phosphorus, we identified candidate phosphate starvation responsive (PSR) genes and developed their intron length polymorphism (ILP) markers in maize on a genome-wide scale. Based on the known plant PSR genes, 161 candidate PSR genes were identified. Of these genes, 138 genes contained at least one intron and were then used to develop 606 PSR-ILP markers by designing PCR primers to the intron-flanking exonic regions. PCR evaluation was performed on 43 randomly selected PSR-ILP markers in 30 maize inbred lines. Of the primers, 88.4% amplified stable and pure products in all maize inbred lines, and 53.5% of the markers showed ILP, with PIC values ranging from 0.06 to 0.80. The result of clustering analysis of the 30 maize inbred lines, based on the polymorphism of 23 ILP markers, suggests that the ILP markers developed in this study are not only efficient for genetic diversity analysis but also potentially useful for marker assisted selection for tolerance to low phosphorus.

Root type and soil phosphate determine the taxonomic landscape of colonizing fungi and the transcriptome of field‐grown maize roots

“…The complete list of differentially expressed genes is provided in Notes S5. Based on previously characterized P starvation‐responsive (PSR) genes of maize (He et al ., ), 25 candidate PSR genes responded significantly to P levels (Fig. b), whereas the other genes determined by He et al .…”

“…b), whereas the other genes determined by He et al . () were not expressed or did not differ in expression between the different conditions. These candidate PSR genes clustered into two groups.…”

“…(b) Expression pattern of P starvation‐responsive ( PSR ) genes in maize root types. In total, 25 PSR genes (He et al ., ) were detected from the list of genes which were differentially expressed among root types. The expression values were normalized by log 2 ‐transformed fragments per kilobase of transcript per million reads ( FPKM ).…”

Root type and soil phosphate determine the taxonomic landscape of colonizing fungi and the transcriptome of field-grown maize roots

“…The complete list of differentially expressed genes is provided in Dataset S5. Based on previously characterized phosphate starvation responsive (PSR) genes of maize (He et al ., 2015), 25 candidate PSR genes significantly responded to phosphate levels (Fig. 4b), while the other genes determined by He et al ., (2015) were not expressed or did not differ in expression between the different conditions.…”

“…(b) Expression pattern of phosphate starvation response (PSR) genes in maize root types. In total, 25 PSR genes (He et al ., 2015) were detected from the list of genes, which are differentially expressed among root types. The expression values were normalized by log 2 transformed FPKM.…”