■辣椒(辣椒属。)是一种全球种植的蔬菜,经过了广泛的驯化,导致其农艺性状显著多样化。随着辣椒基因组学的进步和测序成本的降低,单核苷酸多态性(SNPs)和小插入缺失(indel)的高通量检测对于分析辣椒种质和改进育种计划越来越重要.因此,迫切需要一种具有成本效益的,高通量,适用于辣椒育种前景和背景选择的通用技术。
■在本研究中,基于Python的网络抓取脚本用于从已发表的文献和相关序列数据库中系统地提取数据,重点是辣椒基因组。在数据提取之后,精心鉴定和过滤SNP和indel。这个过程最终导致了核心多态性位点的划定,这对特定探针的开发很有帮助。在此之后,对420份辣椒种质进行了全面的表型和基因型分析。同时,进行了一项全基因组关联研究(GWAS),以阐明辣椒螺旋果实形状的遗传决定因素.
■在这项研究中,在GenoBaits平台上开发了45K辣椒按目标测序基因分型(GBTS)液相基因芯片。这个芯片由45,389个探针组成,其中42,535个来自背景遗传景观中的核心多态位点(CPS),而2,854与前景农艺性状相关,跨越43个特征。CPS探针的平均间隔为68Kb。我们已经评估了该芯片在420份辣椒种质上的性能,通过45,387个探针成功捕获靶DNA片段。此外,在测试的420份种质中,410份中的探针捕获率超过70%。使用这个芯片,我们已经对273份辣椒种质进行了有效的基因分型,并阐明了410份辣椒种质之间的遗传关系。我们的结果允许对姊妹系和中国菜种质进行精确聚类。此外,通过螺旋状水果形状的GWAS,我们确定了三个数量性状基因座(QTL):heli2.1,heli11.1和heli11.2。在heli11.1QTL内,鉴定了编码微管蛋白α链的基因,表明其在辣椒果实螺旋生长模式中的潜在作用。
■总之,45K辣椒GBTS液相基因芯片提供了对多态性位点的强大检测,是推进辣椒种质研究和辣椒新品种育种的有前途的工具。
UNASSIGNED: Pepper (Capsicum spp.) is a vegetable that is cultivated globally and has undergone extensive domestication, leading to a significant diversification in its agronomic traits. With the advancement of genomics in
pepper and the reduction in sequencing costs, the high-throughput detection of single nucleotide polymorphisms (SNPs) and small insertions-deletions (indels) has become increasingly critical for analyzing pepper germplasms and improving breeding programs. As a result, there is a pressing need for a cost-effective, high-throughput, and versatile technique suitable for both foreground and background selection in
pepper breeding.
UNASSIGNED: In the present study, Python-based web scraping scripts were utilized to systematically extract data from published literatures and relevant sequence databases focusing on pepper genomes. Subsequent to data extraction, SNPs and indels were meticulously identified and filtered. This process culminated in the delineation of core polymorphic sites, which were instrumental in the development of specific probes. Following this, comprehensive phenotypic and genotypic analyses were conducted on a diverse collection of 420 pepper germplasms. Concurrently, a genome-wide association study (GWAS) was conducted to elucidate the genetic determinants of helical fruit shape in peppers.
UNASSIGNED: In this study, a 45K
pepper Genotyping-By-Target-Sequencing (GBTS) liquid-phase gene chip was developed on the GenoBaits platform. This chip is composed of 45,389 probes, of which 42,535 are derived from core polymorphic sites (CPS) in the background genetic landscape, while 2,854 are associated with foreground agronomic traits, spanning across 43 traits. The CPS probes are spaced at an average interval of 68 Kb. We have assessed the performance of this chip on 420 pepper germplasms, with successful capture of target DNA fragments by 45,387 probes. Furthermore, the probe capture ratio surpassed 70% in 410 of the 420 germplasms tested. Using this chip, we have efficiently genotyped 273 germplasms for spiciness levels and elucidated the genetic relationships among 410 pepper germplasms. Our results allowed for precise clustering of sister lines and C. chinense germplasms. In addition, through a GWAS for helical fruit shape, we identified three quantitative trait loci (QTLs): heli2.1, heli11.1, and heli11.2. Within the heli11.1 QTL, a gene encoding the tubulin alpha chain was identified, suggesting its potential role in the helical growth pattern of pepper fruits.
UNASSIGNED: In summary, the 45K pepper GBTS liquid-phase gene chip offers robust detection of polymorphic sites and is a promising tool for advancing research into pepper germplasm and the breeding of new
pepper varieties.