A High-Density Genetic Map Constructed for Maize (Zea mays L.) Based on Large-Scale SNP Discovery Using Whole-Genome Resequencing and Specific-Locus Amplified Fragments Sequencing (SLAF-Seq)

IF 0.6 4区生物学 Q4 GENETICS & HEREDITY Russian Journal of Genetics Pub Date : 2024-01-15 DOI:10.1134/s1022795423140107

Q. Chen, J. Song, Z. Nie, G. R. Yu, L. Y. Xu, J. Zhang, Y. Jiang, W.-P. Du

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Abstract

Maize is an important food and industrial material resource. We constructed a high-density genetic map using the whole-genome resequencing and specific-locus amplified fragments sequencing (SLAF-seq) techniques for the “HZS” and “X224M” elite maize inbred lines, and 196 F₂ individuals from a cross between “HZS” and “X224M.” In our study, the average resequencing depth of the maternal and paternal parents was 13.30-fold and 11.94-fold, respectively. In the F₂ population, the sequencing depth ranged from 9.64-fold to 45.16-fold with an average of 23.18-fold. In total, 12, 354, 021 SNPs were detected in the F₂ population, and 87.78% of which were polymorphic. Among these SNPs, 2, 843, 917 (53.96%) were included in the segregation pattern aa × bb. Finally, 6, 186 SNPs were used to construct a high-density genetic map. The length of this map included all 10 chromosomes in maize and was 1, 667.36 cM, with an average distance of 0.318 cM between markers. The number of mapped SNPs in different linkage groups (LGs) ranged from 254 to 960, and the genetic distance of each LGs ranged from 157.22 to 192.72 cM. Based on the evaluation of haplotype and heat maps, the results indicated that our genetic map is of high quality, and we now have more detailed information for gene mapping and marker-assisted breeding.

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利用全基因组重测序和特定病灶扩增片段测序 (SLAF-Seq) 大规模发现 SNP，构建玉米 (Zea mays L.) 的高密度遗传图谱

摘要玉米是重要的粮食和工业原料资源。我们利用全基因组重测序和特定位点扩增片段测序（SLAF-seq）技术，对 "HZS "和 "X224M "玉米近交系以及 "HZS "和 "X224M "杂交的196个F2个体构建了高密度遗传图谱。在我们的研究中，母本和父本的平均重测序深度分别为 13.30 倍和 11.94 倍。在 F2 群体中，测序深度从 9.64 倍到 45.16 倍不等，平均为 23.18 倍。F2 群体中共检测到 12 354 021 个 SNPs，其中 87.78% 为多态性。在这些 SNPs 中，2, 843, 917 个（53.96%）包含在 aa × bb 的分离模式中。最后，6 186 个 SNPs 被用于构建高密度遗传图谱。该图谱包括玉米的所有 10 条染色体，长度为 1,667.36 cM，标记间的平均距离为 0.318 cM。不同连锁群（LGs）中的SNPs数量从254个到960个不等，每个LGs的遗传距离从157.22到192.72 cM不等。根据单体型图和热图的评估，结果表明我们的遗传图谱质量较高，为基因图谱绘制和标记辅助育种提供了更详细的信息。

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来源期刊

Russian Journal of Genetics 生物-遗传学

CiteScore

1.00

自引率

33.30%

发文量

126

审稿时长

1 months

期刊介绍： Russian Journal of Genetics is a journal intended to make significant contribution to the development of genetics. The journal publishes reviews and experimental papers in the areas of theoretical and applied genetics. It presents fundamental research on genetic processes at molecular, cell, organism, and population levels, including problems of the conservation and rational management of genetic resources and the functional genomics, evolutionary genomics and medical genetics.