Genome-wide Association Study Of Cell Wall Components And Forage Quality In Maize Stalk

Maize is the most important staple crop in the world,and it is also a vital forage resource.Cell wall components of maize stalk play an important role in lodging resistance,and also show a big effect on forage palatability and digestibility.Improving forage quality can increase nutrition uptake,thus,the main target of forage maize breeding is to select good forage quality variant.Nowadays,molecular biology and genome-wide association analysis provide us an innovative method for dissecting the genetic architecture of cell wall components and forage digestibility in maize stalk,and support us to better understand the mechanism of cell wall biosynthesis and genetic network.In this study,genome-wide association was used to dissect the genetic basis of cell wall components and forage digestibility in maize stalk.The main results are as following:1.A maize association mapping panel which was consisted of 368 inbred lines were planted in 7 environments and evaluated lignins(LIG),cellulose(CEL),hemicellulose(HC),acid detergent fiber(ADF),neutral detergent fiber(NDF)and in vitro dry matter digestibility(IVDMD).The best linear unbiased predicted(BLUP)value of 6 traits were calculated with a mixed linear model.Phenotypic variation ranged from 1.2 fold(HC)-2.2 fold(IVDMD).The results of analysis of variance suggest that,genetic factors significantly affect phenotypic variance.The heritability estimates of 6 traits were relative high,which ranged from 0.68(HC)to 0.85(IVDMD).2.A total of 559,285 SNPs with minor allele frequency(MAF)greater than 5%were genotyped with DNA chip and RNA-sequencing.A mixed model with population structure and polygenic background effects was fitted to identify associations for cell wall components and forage quality.At a significance level of P<1×10-4 together with a threshold of RMIP>0.1,64 and 69 unique association loci were detected for cell wall components and forage quality traits.Each locus can explain 4.2%-6.7%of the phenotypic variance.These results suggest that,the genetic basis of cell wall components and forage quality were mainly controlled by multiple minor effect genes in this association mapping populations.3.Candidate genes were nominated according to the association loci.ZmC3H2 was found associated with LIG and stalk quality traits.This lignin-pathway gene was found encode a coumarate-3-hydroxylase,which not only controls the ratio between H and G/S type monolignol content,but also show a influence to total lignin content.We also found some transcription factor genes that involved in regulating the expression level of cell wall biosynthesis pathway genes,such as LIM and SND-2/3 like NAC transcription factors.In addition,the other candidate genes mainly included genes encoding stress-induced proteins and enzymes involved in other biology processes.