Association analysis of single nucleotide polymorphisms in candidate genes with root traits in maize (Zea mays L.) seedlings

Abstract

Several genes involved in maize root development have been isolated. Identification of SNPs associated with root traits would enable the selection of maize lines with better root architecture that might help to improve N uptake, and consequently plant growth particularly under N deficient conditions. In the present study, an association study (AS) panel consisting of 74 maize inbred lines was screened for seedling root traits in 6, 10, and 14-day-old seedlings. Allele re-sequencing of candidate root genes Rtcl, Rth3, Rum1, and Rul1 was also carried out in the same AS panel lines. All four candidate genes displayed different levels of nucleotide diversity, haplotype diversity and linkage disequilibrium. Gene based association analyses were carried out between individual polymorphisms in candidate genes, and root traits measured in 6, 10, and 14-day-old maize seedlings. Association analyses revealed several polymorphisms within the Rtcl, Rth3, Rum1, and Rul1 genes associated with seedling root traits. Several nucleotide polymorphisms in Rtcl, Rth3, Rum1, and Rul1 were significantly (P<0.05) associated with seedling root traits in maize suggesting that all four tested genes are involved in the maize root development. Thus considerable allelic variation present in these root genes can be exploited for improving maize root characteristics.

SNP-based association analysis for seedling traits in durum wheat (<i>Triticum turgidum</i> L. <i>durum</i> (Desf.))

“…The root system of plants also should be worthy of close attention because roots play a vital role in plant growth, development, and fitness (Bai et al 2013, Kumar et al 2014). Hydroponics is an excellent method of conducting studies on plant root system under controlled environmental conditions (Bai et al 2013, Canè et al 2014, Liu et al 2013).…”

Genetic dissection of maize seedling root system architecture traits using an ultra‐high density bin‐map and a recombinant inbred line population

“…Efficient and accurate phenotyping protocols are needed to improve identification of quantitative trait loci (QTL) controlling the RSA‐related traits. Direct root architecture phenotyping in the field is difficult and the variability of the soil environment within fields is a concern (Lynch ; Kumar et al ). Paszkowski and Boller () reported that the lateral rootless1 mutant could be complemented by symbiotic microbes and high fertility (Paszkowski and Boller ), indicating the magnitude of a root loci's effect is likely to be mediated by the soil environment.…”

“…Among these, hydroponics has been favored for precise control of nutrient concentration and the ease of phenotyping. Using this method, many QTL controlling lateral root number, primary root length and other traits have been identified at various water and nutrient regimes (Mano et al ; Zhu et al ; Liu et al ; Abdel‐Ghani et al ; Burton et al ; Kumar et al ).…”

Molecular and phenotypic characterization of doubled haploid exotic introgression lines for nitrogen use efficiency in maize

“…Selection for genotypes with a vigorous root system could enhance the adaptation of maize under water and nutrient deficit soils. Although extensive genetic variation for root architecture has been reported Abdel-Ghani et al, 2014;Kumar et al, 2014;, root traits have been seldom considered as selection criteria to improve yield in maize, mainly because characterization of root morphology in the field is laborious, inaccurate and time consuming . Characterization of root traits under hydroponic conditions in this case has the advantage of screening a high number of genotypes in a small space (in a growth chamber) within a short period of time (2-3 weeks).…”

“…5 shows the distribution of GBS and SNP chip markers in Chromosome 10, which shows that, between 10-15 cM, there was no representation of SNP chip markers.…”