摘要
【目的】建立桃单果质量(旧称单果重)性状分子标记辅助选择体系,提高育种效率。【方法】总结现有的单果质量分子标记,并结合574份种质基因组重测序数据,在只考虑位点间加性作用的情况下,分析中国育成品种的单果质量育种值,结合位点效应值筛选用于改良现有品种的亲本材料。【结果】选择了SNP、Indel等有特定染色体位置的标记,共46个。结合实验室前期的574份桃栽培品种重测序的遗传变异信息、连锁不平衡和偏分离信息,筛得19个效应值呈现显著异质性的标记位点。对3个优良品种(中油蟠7号、中油蟠15号和华光)育种过程中亲本材料的基因型效应解析发现,中油蟠7号和中油蟠15号在选育过程中,亲本材料的育种值略有起伏,但整体呈现持续增大趋势,而华光在育成过程中,单果质量的育种值呈现直线下降趋势。通过分析目前主栽的30个品种,发现预测效应值与真实观测值之间呈极显著正相关。利用所筛标记从地方品种中筛选对主栽品种有改良意义的亲本种质,如长岭早玉露、白花等。【结论】该研究初步建立了包含19个分子标记的桃单果质量性状分子辅助选择体系,利用其基因型效应值进行叠加计算,可实现对桃单果质量表型的早期预测。
【Objective】The fruit weight of peaches is a quantitative trait influenced by multiple genes.This paper provides a comprehensive summary of the molecular markers associated with fruit weight,which have been identified in previous studies.It also evaluates the breeding value of fruit weight in cultivated varieties in China,focusing exclusively on the additive effects between loci.Furthermore,this study identifies and recommends parental materials that can be utilized to improve existing varieties.【Methods】Building on both domestic and international research advancements,this study synthesized the molecular markers associated with fruit weight as identified by previous researchers.Utilizing the 574 genome resequencing data generated by our team,we employed Trimmomatic software to ensure the quality control of the raw sequencing data,resulting in filtered sequences.Subsequently,BWA software facilitated sequence alignment,while GATK software was employed for variant detection,ultimately enabling the determination of each variety's genotype.Genotypic effect values were calculated as follows:the allelic effects of SNP loci on traits were estimated by comparing the phenotypic values of different genotypes[homozygous reference(0/0),heterozygous(0/1),and homozygous mutant(1/1)]in pairs.Alleles were classified as positive if there was a significant increase in phenotypic values between the homozygous reference and other genotypes;otherwise,they were classified as negative.Additionally,we screened and recommended parental materials for the improvement of current varieties by incorporating locus effect values.【Results】Drawing upon research advancements both domestically and internationally,this study identified markers with specific chromosomal locations,including SNPs and Indels,ultimately selecting 46 markers from eight research teams.An analysis of marker positions revealed that the numbers of markers on chromosomes 1 through 8 were 5,6,4,9,3,12,2,and 5,respectively,indicating a higher concentration of loci on chromosomes 4 and 6.Utilizing genetic variation data from 574 peach cultivars collected in the initial phase of laboratory research,the linkage disequilibrium(LD)of the germplasm was calculated.The physical distance at which the LD intensity(r2)decayed to a standard level was used as the threshold for merging loci,resulting in a reduction of loci to 25.Additionally,19 marker sites were identified after excluding 6 markers that were significantly divergent from the germplasm.These loci can be utilized to assess their contribution to the trait of fruit weight in natural populations,with the effect values of these 19 loci exhibiting significant heterogeneity.Among these,three loci(N3,N10,and N19)exhibited strong positive effects,with the N3 locus at the terminus of chromosome 1 showing the highest effect value of 10.86.Conversely,five loci(N11,N13,N15,N16,and N17)demonstrated strong negative effects,with the N15 locus at the apex of chromosome 6 having the lowest effect value of-20.06.Neutral effect sites,with values ranging from-1.72 to 1.04,constituted 36.84%of the total.With three superior varieties(Zhongyoupan 7,Zhongyoupan 15,and Huaguang),the breeding values of the parents of Zhongyoupan 7 and Zhongyoupan 15 exhibited minor fluctuations throughout the breeding process;however,the overall trajectory was upward.In contrast,during the breeding of Huaguang,the breeding value for fruit weight showed a linear decline,aligning with the downward trend observed in the actual fruit weight phenotype during the breeding process.Furthermore,an analysis of the 30 principal varieties currently under cultivation revealed a highly significant positive correlation between the predicted effect values and the actual observed values,with an R2 of 0.4673(r_(0.01,28)=0.4628,P=3.1250E-05).Among these 30 main varieties,24 exhibited negative effects at the N15 locus,which had the highest effect value,and 19 exhibited negative effects at the N13 locus,which had the second highest effect value.Consequently,all these varieties can be hybridized with germplasm(including wild germplasm,local varieties,or other breeding varieties)possessing the mutation site,and the molecular marker-assisted selection can be conducted through genotype identification.Utilizing the identified markers,the parent germplasm with significant improvement potential for key cultivated varieties,such as Changling Zaoyulu,Jinlin 8903,Wanpantao,Jietubai and Baihua,was selected from local varieties.【Conclusion】In conclusion,this study identified and screened 19 markers associated with fruit weight,and their effect values were aggregated.The breeding values of the parent materials and 30 primary varieties were calculated during the cross-breeding process of three different varieties.The results demonstrated a correlation between the breeding values and the observed phenotype of fruit weight,thereby confirming that these markers are applicable in molecular-assisted breeding for enhancing fruit weight,which realized the early prediction of fruit weight phenotype of peach.
作者
别航灵
李勇
陈昌文
方伟超
王力荣
曹珂
BIE Hangling;LI Yong;CHEN Changwen;FANGWeichao;WANG Lirong;CAO Ke(Zhengzhou Fruit Research Institute,CAAS,Zhengzhou 450009,Henan,China;Zhongyuan Research Center,CAAS,Xinxiang 453003,Henan,China)
出处
《果树学报》
北大核心
2026年第3期481-492,共12页
Journal of Fruit Science
基金
国家自然科学基金项目(32272673)
中国农业科学院科技创新工程专项(CAAS-ASTIP-2025-ZFRI)。
关键词
桃
单果质量
基因型鉴定
育种值分析
亲本选择
Peach
Fruit weight
Genotyping
Breeding value analysis
Parental selection
