QTL Analysis for Seeding Traits Related to Low Nitrogen Tolerance in Foxtail Millet

The analysis of quantitative trait loci (QTL) related to low nitrogen tolerance traits of millet (Setaria italica L.) laid a foundation for fine mapping, cloning and functional research of low nitrogen tolerance genes. At the same time, it also provided technical support for revealing the genetic mechanism of low nitrogen tolerance of millet and breeding low nitrogen tolerance varieties.

The recombinant inbred line (RIL) population consisting of 120 family lines was used as experimental materials, that was constructed from parents Yugu 28, a low nitrogen tolerant variety, and Qiyehuang, a low nitrogen sensitive variety. The RIL populations were treated with low nitrogen and normal nitrogen at seedling stage, and seven traits were analyzed of hydroponic for 21 days, which inculding seedling length, maximum root length, root dry weight, seedling dry weight, plant dry weight, relative chlorophyll content and plant nitrogen content. At the same time, we used composite interval mapping (CIM) to locate and analyze QTLs for traits related to low nitrogen tolerance, and predicted the candidate genes in the confidence intervals of QTL_S.

The traits associated with low nitrogen tolerance of RIL populations exhibited continuous distribution with apparent transgressive segregation both under low nitrogen and normal nitrogen levels, which conformed to the typical genetic characteristics of quantitative traits and were suitable for QTL genetic analysis. Correlation analysis showed that seeding length was positively correlated with maximum root length, root dry weight, seeding dry weight, plant dry weight and relative chlorophyll content, and maximum root length was negatively correlated with plant nitrogen content. A total of thirty-four QTLs related to seeding length, maximum root length, root dry weight, seeding dry weight, plant dry weight, relative chlorophyll content and plant nitrogen content were located under low nitrogen and normal nitrogen levels, which distributed on chromosomes from 1 to 9. They explained individually 5.15%-52.42% phenotypic variation. Ten QTLs were simultaneously detected under both two nitrogen levels, eleven and thirteen QTLs were only identified under single low nitrogen and normal nitrogen conditions, respectively. A total of fifteen QTLs were major QTL, and five major QTLs were repeatedly detected under both two nitrogen levels, which including qRDW3, qMRL1.1, qMRL1.2, qSL5 and qSPAD1. Five QTL overlaps were detected with gathering multiple QTLs under two nitrogen levels. Six candidate genes related to nitrogen metabolism were identified from the confidence interval of the five QTL overlaps, suggesting that genes related to nitrogen assimilation, absorption and utilization probably control the expression of these genes.

Thirty-four QTLs were scattered on sixteen clusters of nine chromosomes. Based on gene annotation, a total of 6 candidate genes related to nitrogen metabolism were screened in foxtail millet, indicating the different traits involved in common genetic mechanisms, and the favorable alleles for low nitrogen tolerance can be polymerized by marker-assisted selection.