Yousaf Muhammad Farhan, Demirel Ufuk, Naeem Muhammad, Çalışkan Mehmet Emin
Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, 51240 Nigde, Turkey.
3 Biotech. 2021 Apr;11(4):174. doi: 10.1007/s13205-021-02727-6. Epub 2021 Mar 18.
Tuber crops have measurable biological variation in root and stolon phenotyping and thus may be utilized to identify genomic regions associated with these variations. This is the first comprehensive association mapping study related to potato root and stolon traits. A diverse panel of 192 tetraploid potato ( L.) genotypes were grown in aeroponics to reveal a biologically significant variation and detection of genomic regions associated with the root and stolon traits. Phenotyping of root traits was performed by image analysis software "WinRHIZO" (a root scanning method), and stolon traits was measured manually, while SolCAP 25K potato array was used for genotyping. Significant variation was observed between the potato genotypes for root and stolon traits along with high heritabilities (0.80 in TNS to 0.95 in SL). For marker-trait associations, + linear mixed model was implemented and 50 novel genomic regions were detected. Significantly associated SNPs with stolon traits were located on chr 4, chr 6, chr 7, chr 9, chr 11 and chr 12, while those linked to root traits on chr 1, chr 2, chr 3, chr 9, chr 11, and chr 12. Structure and PCA analysis grouped genotypes into four sub-populations disclosing population genetic diversity. LD decay was observed at 2.316 Mbps ( = 0.29) in the population. The identified SNPs were associated with genes performing vital functions such as root signaling and signal transduction in stress environments (GT-2 factors, protein kinases SAPK2-like and protein phosphatases ""), transcriptional and post-transcriptional gene regulation (RNA-binding proteins), sucrose synthesis and transporter families (UGPase, , , and ) and PVY resistance (). The findings of our study can be employed in future breeding programs for improvement in potato production.
The online version contains supplementary material available at 10.1007/s13205-021-02727-6.
块茎作物在根和匍匐茎表型上具有可测量的生物学变异，因此可用于识别与这些变异相关的基因组区域。这是第一项与马铃薯根和匍匐茎性状相关的全面关联图谱研究。在气培条件下种植了由192个四倍体马铃薯（L.）基因型组成的多样化群体，以揭示生物学上显著的变异并检测与根和匍匐茎性状相关的基因组区域。根性状的表型分析通过图像分析软件“WinRHIZO”（一种根扫描方法）进行，匍匐茎性状则通过手动测量，同时使用SolCAP 25K马铃薯阵列进行基因分型。在马铃薯基因型之间观察到根和匍匐茎性状的显著变异以及高遗传力（从TNS中的0.80到SL中的0.95）。对于标记-性状关联，实施了+线性混合模型，并检测到50个新的基因组区域。与匍匐茎性状显著相关的单核苷酸多态性（SNP）位于第4、6、7、9、11和12号染色体上，而与根性状相关的SNP位于第1、2、3、9、11和12号染色体上。结构和主成分分析（PCA）将基因型分为四个亚群，揭示了群体遗传多样性。在该群体中观察到连锁不平衡（LD）衰减发生在2.316兆碱基对处（r² = 0.29）。所鉴定的SNP与在应激环境中执行重要功能的基因相关联，如根信号传导和信号转导（GT-2因子、类SAPK2蛋白激酶和蛋白磷酸酶）、转录和转录后基因调控（RNA结合蛋白）、蔗糖合成和转运蛋白家族（UGPase、、、和）以及马铃薯Y病毒（PVY）抗性（）。我们研究的结果可用于未来的育种计划，以提高马铃薯产量。
在线版本包含可在10.1007/s13205-021-02727-6获取的补充材料。
