Genetic Basis Of Artificial Selection Response In High-Oil Maize

High-oil maize is a product of artificial selection,and is a valuable material for studying the genetic basis of complex quantitative traits in maize.As an important quality trait in maize,oil is not only rich in unsaturated fatty acids,but also rich in antioxidants such as vitamin E and phytosterol esters,which makes maize oil as a healthy vegitable oil.High-oil maize is also an important feed source for poultry and livestock due to high energy.In this study,three generations(C1,C4 and C7)of LvDaHongGu High-Oil(LDHGHO)population,derived from 9 inbred lines,were used to carry out a genome-wide scan to detect selection effects on oil content and other agronomic traits using multiple methods in modern genomics,population genetics and quantitative genetics.These results will provide deep understanding of the genetic basis and dynamic changes of the kernel oil content and other traits in high-oil maize that varied during short-term selection,and consequently provide useful information for the genetic improvement of high-oil maize.The major results are listed as follows:1.The LDHGHO population,including 100,150 and 150 individuals in C1,C4,C7 generations,together with nine parents,were planted in three environments,and six oil-related traits and 16 agronomic traits were measured.Abundant phenotypic variation were observed in the LDHGHO population across three generations,with 3.3-fold difference in kernel oil content.The broad-sense heritability of all identified traits are over 0.8 except days to silk and ear length(?0.7).With the increase of selection cycles,the kernel oil content increased from 4.71%in the Cl generation to 9.38%in the C7 generation,with an average increase of 0.66%per generation.At the same time,other oil-related and agronomic traits were also changed during the selection for oil content,such as earlier flowering time,increased plant height and ear height,and reduced 100-kernel weight.2.All 400 offsprings and their founders were genotyed by whole-genome resequencing,yielding a total of 1675 Gb data with an average resequencing depth of?1.5 × for offspring and?5 × for founder.A total of 4,785,646 high-quality SNPs were mined,which accuracy were estimated to be 97.6%when compared with the SNPs genotyped by a MaizeSNP3K chip.3.To identify the selective signals during the development of high-oil maize,both XP-CLR and FST methods were performed,which were based on extreme allele frequency differentiation considering multiple sites and intergenerational differentiation,respectively.A total of 78 candidate selective regions were detected,accounting for 13%of the genome.The size of selected regions range from 25kb to 31.1Mb.Among them,38 selective regions were detected between C1 and C4,40 were detected between C4 and C7,and 45 were detected between C1 and C1.According to the frequency of the favorable alleles in the selected regions across different generations,four selection patterns were detected:(1)The favorable alleles increased rapidly in the early generation,but slowly in the late generation;(2)the favorable alleles increased slowly in the early generation,but quickly in the late generation;(3)the favorable alleles increased rapidly in the early generation,and tended to be stable in the late generation;(4)the favorable alleles remained constant in the early generation and increased rapidly in the late generation.These results indicate that the accumulation of favorable allele plays a crititical role in contributing to the oil increase during the development of high-oil maize,and the generation and intensity of the accumulation varied among the selected regions.In addition,the expected heterozygosity of each selected region across different generations were compared,52 loci do not demonstrate a significant decrease in heterozygosity in the C7 generation,which suggests that there is a great potential for the increase of kernel oil content in LDHGHO population.4.Genome-wide association analysis using FarmCPU and GEMMA identified a total of 12 to 36 loci significantly associated with each measured trait,with total explained phenotypic variation ranging from 39.7%to 92.1%.Among these loci,36 loci were significantly associated with kernel oil content,and explained 92.1%of the phenotypic variation that is comparable to the broad-sense heritability.Co-localization analysis with selected regions revealed that 2-16 significant association loci for each trait fell within the selected regions.44.4%(16/36)of the loci associated with oil content were selected by 4 different patterns during the selection process.29.5%(23/78)of the selected regions were co-localized with loci associated with multiple traits(?2),indicating that the selection of kernel oil content leads to the selection of other traits partly because of the genetic hitch-hiking effect.For example,the selected region,5-22Mb on chromosome 2,was co-localized with significantly associated loci of 9 traits.GRMZM2G022563 and GRMZM2G016705 are candidate genes for controlling the oil content and 100-kernel weight in this selected region,respectively.The function of GRMZM2G016705 was verified by using UniformMu line with the W22 background.In summary,the dynamic genomic changes indicated that the accumulation of favorable alleles with various patterns play a critical role in the increase of oil content during the selection of High-oil maize.The genetic hitch-hiking effect partly explained the reason why the selection of oil content often accompanied with other agronomic traits.