Yunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming, 650224, China.
College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, China.
BMC Plant Biol. 2024 Jun 10;24(1):524. doi: 10.1186/s12870-024-05122-4.
Amylose, a prebiotic found in yams is known to be beneficial for the gut microflora and is particularly advantageous for diabetic patients' diet. However, the genetic machinery underlying amylose production remains elusive. A comprehensive characterization of the genetic basis of amylose content in yam tubers is a prerequisite for accelerating the genetic engineering of yams with respect to amylose content variation.
To uncover the genetic variants underlying variation in amylose content, we evaluated amylose content in freshly harvested tubers from 150 accessions of Dioscorea zingibensis. With 30,000 high-quality single nucleotide polymorphisms (SNP), we performed a genome-wide association analysis (GWAS). The population structure analysis classified the D. zingiberensis accessions into three groups. A total of 115 significant loci were detected on four chromosomes. Of these, 112 significant SNPs (log10(p) = 5, q-value < 0.004) were clustered in a narrow window on the chromosome 6 (chr6). The peak SNP at the position 75,609,202 on chr6 could explain 63.15% of amylose variation in the population and fell into the first exon of the ADP-glucose pyrophosphorylase (AGPase) small subunit gene, causing a non-synonymous modification of the resulting protein sequence. Allele segregation analysis showed that accessions with the rare G allele had a higher amylose content than those harboring the common A allele. However, AGPase, a key enzyme precursor of amylose biosynthesis, was not expressed differentially between accessions with A and G alleles. Overexpression of the two variants of AGPase in Arabidopsis thaliana resulted in a significantly higher amylose content in lines transformed with the AGPase-G allele.
Overall, this study showed that a major genetic variant in AGPase probably enhances the enzyme activity leading to high amylose content in D. zingiberensis tuber. The results provide valuable insights for the development of amylose-enriched genotypes.
在山药中发现的一种益生元直链淀粉，已知对肠道微生物群有益，尤其对糖尿病患者的饮食有益。然而，直链淀粉产生的遗传机制仍然难以捉摸。全面描述山药块茎直链淀粉含量的遗传基础是加速基于直链淀粉含量变化的山药遗传工程的前提。
为了揭示直链淀粉含量变化的遗传变异，我们评估了 150 份盾叶薯蓣新鲜收获块茎的直链淀粉含量。利用 30000 个高质量的单核苷酸多态性 (SNP)，我们进行了全基因组关联分析 (GWAS)。群体结构分析将盾叶薯蓣品系分为三组。在四条染色体上共检测到 115 个显著位点。其中，在第 6 号染色体 (chr6) 上的一个狭窄窗口中，112 个显著 SNP (log10(p)=5,q-value<0.004) 聚集在一起。chr6 上 75,609,202 位置的峰 SNP 可以解释群体中 63.15%的直链淀粉变异，并且落入 ADP-葡萄糖焦磷酸化酶 (AGPase) 小亚基基因的第一个外显子中，导致产生的蛋白质序列发生非同义修饰。等位基因分离分析表明，具有罕见 G 等位基因的品系的直链淀粉含量高于携带常见 A 等位基因的品系。然而，AGPase 是直链淀粉生物合成的关键酶前体，在具有 A 和 G 等位基因的品系之间没有差异表达。在拟南芥中过表达两种 AGPase 变体，导致转化为 AGPase-G 等位基因的系中直链淀粉含量显著升高。
总的来说，这项研究表明，AGPase 中的一个主要遗传变异可能增强了酶活性，导致盾叶薯蓣块茎中直链淀粉含量升高。结果为富含直链淀粉的基因型的开发提供了有价值的见解。
