Topu Mustafa, Sesiz Uğur, Bektaş Harun, Toklu Faruk, Özkan Hakan
Department of Biotechnology, Institute of Natural and Applied Sciences, Çukurova University, 01330 Adana, Turkey.
Department of Field Crops, Faculty of Agriculture, Çukurova University, 01330 Adana, Turkey.
Life (Basel). 2023 Jul 18;13(7):1579. doi: 10.3390/life13071579.
Simple sequence repeats (SSRs) are highly versatile markers in genetic diversity analysis and plant breeding, making them widely applicable. They hold potential in lentil () breeding for genetic diversity analysis, marker-assisted selection (MAS), and linkage mapping. However, the availability and diversity of SSR markers in lentil is limited. We used next-generation sequencing (NGS) technology to develop SSR markers in lentil. NGS allowed us to identify regions of the lentil genome that contained SSRs. Illumina Hiseq-2000 sequencing of the lentil genotype "Karacadağ" resulted in 1,727,734 sequence reads comprising more than 48,390 Mb, and contigs were mined for SSRs, resulting in the identification of a total of 8697 SSR motifs. Among these, dinucleotide repeats were the most abundant (53.38%), followed by trinucleotides (30.38%), hexanucleotides (6.96%), tetranucleotides (6.59%), and pentanucleotides (3.19%). The most frequent repeat in dinucleotides was the TC (21.80%), followed by the GA (17.60%). A total of 2000 primer pairs were designed from these motifs, and 458 SSR markers were validated following their amplified PCR products. A linkage map was constructed using these new SSRs with high linkage disequilibrium (209) and previously known SSRs (11). The highest number of SSR markers (43) was obtained in LG2, while the lowest number of SSR markers (19) was obtained in LG7. The longest linkage group (LG) was LG2 (86.84 cM), whereas the shortest linkage group was LG7 (53.46 cM). The average length between markers ranged from 1.86 cM in LG1 to 2.81 cM in LG7, and the map density was 2.16 cM. The developed SSRs and created linkage map may provide useful information and offer a new library for genetic diversity analyses, linkage mapping studies, and lentil breeding programs.
简单序列重复（SSRs）是遗传多样性分析和植物育种中用途广泛的标记，具有广泛的适用性。它们在兵豆遗传多样性分析、标记辅助选择（MAS）和连锁图谱构建方面具有潜力。然而，兵豆中SSR标记的可用性和多样性有限。我们利用下一代测序（NGS）技术开发兵豆中的SSR标记。NGS使我们能够识别兵豆基因组中包含SSR的区域。对兵豆基因型“Karacadağ”进行Illumina Hiseq - 2000测序，产生了1,727,734条序列读数，总计超过48,390 Mb，并从重叠群中挖掘SSR，共鉴定出8697个SSR基序。其中，二核苷酸重复最为丰富（53.38%），其次是三核苷酸（30.38%）、六核苷酸（6.96%）、四核苷酸（6.59%）和五核苷酸（3.19%）。二核苷酸中最常见的重复是TC（21.%), 17.60%）。从这些基序中设计了总共2000对引物，并根据其扩增的PCR产物验证了458个SSR标记。利用这些具有高连锁不平衡的新SSR（209个）和先前已知的SSR（11个）构建了连锁图谱。在LG2中获得的SSR标记数量最多（43个），而在LG7中获得的SSR标记数量最少（19个）。最长的连锁群（LG）是LG2（86.84 cM），而最短的连锁群是LG7（53.46 cM）。标记之间的平均长度在LG1中为1.86 cM，在LG7中为2.81 cM，图谱密度为2.16 cM。开发的SSR和创建的连锁图谱可能提供有用信息，并为遗传多样性分析、连锁图谱研究和兵豆育种计划提供新的文库。
