Mukhebi Dennis Wamalabe, Gachanja Pauline Wambui, Karan Diana Jepkoech, Kamau Brenda Muthoni, King'ori Pauline Wangeci, Juma Bicko Steve, Mbinda Wilton Mwema
Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya.
Pwani University Bioscience Research Center (PUBReC), Pwani University, Kilifi, Kenya.
PLoS One. 2025 Jan 31;20(1):e0313850. doi: 10.1371/journal.pone.0313850. eCollection 2025.
Cashew (Anacardium occidentale L.) is an important tree grown worldwide for its edible fruits, nuts and other products of industrial applications. The ecologically sensitive cashew-growing region in coastal Kenya is significantly affected by rising temperatures, droughts, floods, and shifting rainfall patterns. These changes adversely impact cashew growth by altering flowering patterns, increasing pests and diseases, and causing postharvest losses, which ultimately result in reduced yields and tree mortality. This is exacerbated by the long juvenile phase, high heterozygosity, lack of trait correlations, large mature plant size, and inadequate genomic resources. For the first time, the Diversity Array Technology (DArT) technology was employed to identify DArT (silicoDArT) and single nucleotide polymorphisms (SNPs) markers for genomic understanding of cashew in Kenya. Cashew leaf samples were collected in Kwale, Kilifi and Lamu counties along coastal Kenya followed by DNA extraction. The reduced libraries were sequenced using Hiseq 2500 Illumina sequencer, and the SNPs called using DarTsoft14. A total of 27,495 silicoDArT and 17,008 SNP markers were reported, of which 1340 silicoDArT and 824 SNP markers were used for analyses after screening, with > 80% call rate, > 95% reproducibility, polymorphism information content (PIC ≥ 0.25) and one ratio (>0.25). The silicoDArT and SNP markers had mean PIC values ranging from 0.02-0.50 and 0.0-0.5, with an allelic richness ranging from 1.992 to 1.994 for silicoDArT and 1.862 to 1.889 for SNP markers. The observed heterozygosity and expected values ranged from 0.50-0.55 and 0.34-0.37, and 0.56-0.57 and 0.33 for both silicoDArT and SNP markers respectively. Understanding cashew genomics through the application of SilicoDArT and SNP markers is crucial for advancing cashew genomic breeding programs aimed at improving yield and nut quality, and enhancing resistance or tolerance to biotic and abiotic stresses. Our study presents an overview of the genetic diversity of cashew landraces in Kenya and demonstrates that DArT systems are a reliable tool for advancing genomic research in cashew breeding.
腰果（Anacardium occidentale L.）是一种重要的树木，在全球范围内种植，用于其可食用的果实、坚果以及其他工业应用产品。肯尼亚沿海生态敏感的腰果种植区受到气温上升、干旱、洪水和降雨模式变化的显著影响。这些变化通过改变开花模式、增加病虫害以及导致收获后损失，对腰果生长产生不利影响，最终导致产量下降和树木死亡。漫长的幼年期、高杂合性、缺乏性状相关性、成熟植株体型大以及基因组资源不足，使情况更加恶化。首次采用多样性阵列技术（DArT）来鉴定用于肯尼亚腰果基因组研究的DArT（电子DArT）和单核苷酸多态性（SNP）标记。在肯尼亚沿海的夸莱、基利菲和拉穆县采集了腰果叶片样本，随后进行DNA提取。使用Hiseq 2500 Illumina测序仪对简化文库进行测序，并使用DarTsoft14调用SNP。共报告了27495个电子DArT和17008个SNP标记，筛选后使用了1340个电子DArT和824个SNP标记进行分析，其检出率>80%、重复性>95%、多态性信息含量（PIC≥0.25）且比例>0.25。电子DArT和SNP标记的平均PIC值范围分别为0.02 - 0.50和0.0 - 0.5，电子DArT的等位基因丰富度范围为1.992至1.994，SNP标记为1.862至1.889。电子DArT和SNP标记的观察杂合度和预期值范围分别为0.50 - 0.55和0.34 - 0.37，以及0.56 - 0.57和0.33。通过应用电子DArT和SNP标记来了解腰果基因组学，对于推进旨在提高产量和坚果品质、增强对生物和非生物胁迫的抗性或耐受性的腰果基因组育种计划至关重要。我们的研究概述了肯尼亚腰果地方品种的遗传多样性，并证明DArT系统是推进腰果育种基因组研究的可靠工具。
