| Phosphorus is an essential macronutrient,which plays a pivotal role in the growth and fecundity of plants.Phosphate ion forms insoluble compounds readily with metallic ions in the soil,making phosphorus difficulty to be absorbed and utilized.Therefore,deficiency of available phosphorus in topsoil is always the constraint for yield improvement.Unlocking the genetic basis of low-phosphorus tolerance,evaluating and selecting the germplasm and breeding varieties with high phosphorus use efficiency become a paramount solution to resolve the “P crisis”.Low-phosphorus stress will result in inhibited maize(Zea mays,L.)growth,delayed flowering time,decreased grain number and finally the loss of production.This research was designed to elucidate the genetic mechanism of low-phosphorus tolerance in maize by combining multi-methods of genetic analysis,including genome-wide association study,bulked sample analysis of DNA,RNA-seq and genomic selection.The results are provided as follows:1.To evaluate the maize 55 K array for its suitability to molecular breeding and this research,we genotyped 593 inbred lines with the following results obtained:(1)Compared with other SNP chips,the 55 K array had lower missing and heterozygous rates.(2)This 55 K array could clearly distinguish from each other of the major maize heterotic groups in China.(3)The SNP design of 55 K array was not biased towards tropical or temperate maize germplasms and this array included more SNPs with a lower minor allele frequency in tropical maize,facilitating the detection of rare but valuable genes/alleles in tropical germplasm resources and the decipherment of maize genetic mechanism for low-phosphorus stress tolerance.2.Two association populations,genotyped by the 55 K SNPs,were evaluated in the field in Gansu and Guangdong.Based on the relative phenotypic value between low-phosphorus and normal phosphorus conditions,grain weight per plant,grain number and grain number per row were found to be the top three traits that were affected most by low-phosphorus stress.Among the major groups of maize in China,SPT group showed better low-phosphorus tolerance and wide adaptability while Iodent group exhibited greater yield potential under low-phosphorus condition.3.In total,300 candidate genes were identified under two phosphorus conditions using Farm CPU method.The genes detected under low-phosphorus condition are mainly involved in four major pathways: transcriptional regulation,reactive oxygen scavenging,hormone regulation and remodeling of cell wall.Using transcriptome data of the extreme inbred lines,118 genes with differential expression were detected,which were not only differentially expressed during seedling stages,but also significantly associated with flowering and yield traits.Weighted gene co-expression network analysis identified two gene modules associated with fresh weight of shoot and root,activity of acid phosphatase and anthocyanin content.Ten key genes in the two gene modules were overlapped with those identified under low-phosphorus condition.Haplotype analysis revealed that the average grain number of positive haplotypes increased by 41.2% than that of negative haplotypes under low-phosphorus condition.To make the results of genome-wide association study applicable in molecular breeding,five genomic selection methods were compared for their predictive abilities,suggesting that two of the methods,RR-BLUP and GBLUP,outperformed the others under normal and low-phosphorus conditions.Moreover,integrating genome-wide association study results into genomic selection models significantly improved the prediction accuracy.4.Using an F2:3 population,45 significant SNPs and 6 candidate gene regions were identified through DNA bulk sample analysis of the extreme phenotypes.As revealed by genome-wide association study and RNA-seq,candidate genes within these regions were mainly involved in the metabolic processes of reactive oxygen scavenging and transcription regulation. |
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