Genetic Analysis Of Maize(Zea Mays L.) Root System Architecture In Top Soil And The Relationship With Nitrogen Use Efficiency

Root is a key organ for crops to absorb nutrients and water. Genetic improvement of roots is of great significance in terms of high yield and high resources efficiency in crops. However, the natural variation of root system architecture among the different maize germplasms, and their relationships to nitrogen use efficiency remains uncertain, particularly under field conditions. Additionally, the genetic mechanism underlying establishment of root system architecture needs to be further studied. This work applied an advanced high-throughput method DIRT (Digital Image of Root Traits) to evaluated maize root traits in field using an association population of approx.500 lines and 159 imported US commercial inbred lines. An evaluation of root system architecture at top soil layer (0-20 cm) were performed at both silking and maturation stages at four locations including Hainan, Beijing, Henan and Hebei. The genetic association between root system architecture and nitrogen use efficiency was also examined, with the use of the imported US commercial inbred lines under two nitrogen regimes. Meanwhile, in order to uncover the genetic mechanism underlying root traits, a genome-wide association analysis (GWAS) of maize root system architecture was conducted using the root traits phenotyped within the associated panel at silking and maturation stages. The main results are presented as belows:1. With 508 lines association panel, we found the extensive genetic variations for the traits of root system architecture with high broad-sense heritability, which ranged from 54.9% to 83.0% and the coefficiency of variation ranged from 3.7%-63.6% at silking stage.2. The root phenotype was compared between inbred lines from China and US GEM project. The root projected area (RPA), root max width (RMAW) and root bottom angle (RBA) of Chinese inbred lines were significantly higher than those of the US GEM inbred lines at both silking and maturation stage. No significant difference was found between the root average density (RAD) and root top angle (RTA), Chinese lines showed higher root med width (RMEW) than that of US GEM lines at silking stage, but not maturation stage. Since both association panel and 159 US commercial lines were planted in the same location (Hainan), we performed the direct comparison about their root traits at the maturation stage. The results showed that root projected area (RPA) of the US commercial lines was larger than that of Chinese by 12.4%, while root average density (RAD), root med width (RMEW) and root top angle (RTA) of the US commercial lines were less than those of Chinese.3. Chinese lines were further assigned into different heterotic subgroups. The root projected area (RPA) of SPT heterotic subgroup at silking stage was significantly less than that of the PA and LRC subgroup by around 20%. Root max width (RMAW) and root bottom angle (RBA) of SPT were also significantly lower than that of the LAN subgroup by approximately 19%. The root average density (RAD) of the LRC subgroup was significantly higher than that of SPT and PB subgroup. The root top Angle (RTA) did not differ significantly among these five heterotic subgroups.4. The GWAS analysis revealed that 11 and 14 SNPs were remarkably associated with the traits of root system architecture at silking and maturation stage, respectively. GWAS analysis at silking stage found that a candidate gene lied in chromosome BIN5.03, which controled the angle and extension width of the root. By phenotypic correlation, principal component analysis and cluster analysis, a strong correlation was observed between root projected area and root width extension(r=0.78). The significant differences were also shown between the traits of root projected area and root density. Furthermore, none of any SNP for traits of root projected area and root density was co-localized.5. A significant correlation was shown between the root projected area (RPA) and nitrogen uptake efficiency (NupE) at silking stage under both N levels (r=0.35-0.45). The principal component analysis showed that root projected area (RPA) was closely related to the straw yield and NupE. The root top angle (RTA) was also closely related to the yield particularly under low nitrogen conditions. With the increase of root projected area, grain yield and straw yield also increased, especially under low nitrogen conditions. Similarly, the increase of the root average density led to increate of yield, but its positive contribution disappeared when it increased to the certain threshold.6. The 159 US commercial lines were assigned into four groups based on the phenotype related to NUE. The root projected area, root average density and root width extension increased in group of high yield at both N levels (EE) and group of high yield at high N level. Under low nitrogen condition, the root top angle of HNE group significantly decreased.Taken together, our study suggested the presence of large natural variation of root traits among the different germplasms, including association population and imported US commercial inbred lines. Compared with the Chinese lines, the US commercial lines had roots with larger size but smaller width extension, which enabled to form deeper rooting. A close genetic relationship was also determined between root size and NupE. Root density might have distinct genetic basis from root size, which showed less contribution to NUE. Finally, GWAS revealed several valuable SNPs closely linked with root traits. These results provided the valuable knowledge on genetic variation of root system architecture, allowing to genetically improve nitrogen use efficiency in maize.