Camelina (Camelina sativa), an allohexaploid species, is an emerging aviation biofuel crop that has been the focus of resurgent interest in recent decades. To guide future breeding and crop improvement efforts, the community requires a deeper comprehension of subgenome dominance, often noted in allopolyploid species, alongside and understanding of the genetic diversity and population structure of material present within breeding programs. We conducted population genetic analyses of a C. sativa diversity panel, leveraging a new genome, to estimate nucleotide diversity and population structure, and analyzed for patterns of subgenome expression dominance among different organs. Our analyses confirm that C. sativa has relatively low genetic diversity, and show that the SG3 subgenome has substantially lower genetic diversity compared to the other two subgenomes. Despite the low genetic diversity, our analyses identified thirteen distinct subpopulations including two distinct wild populations and others putatively representing founders in existing breeding populations. When analyzing for subgenome composition of long non-coding RNAs, which are known to play important roles in (a)biotic stress tolerance, we found that the SG3 subgenome contained significantly more lincRNAs compared to other subgenomes. Similarly, transcriptome analyses revealed that expression dominance of SG3 is not as strong as previously reported, and may not be universal across all organ-types. From a global analysis, SG3 was only significant higher expressed in flower, flower bud, and fruit organs, which is an important discovery given that the crop yield is associated with these organs. Collectively, these results will be valuable for guiding future breeding efforts in camelina.

中文翻译：

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探索同种异体多倍体 Camelina sativa 的遗传多样性、种群结构和亚基因组差异：对未来育种和研究的影响


Camelina （Camelina sativa） 是一种异体六倍体物种，是一种新兴的航空生物燃料作物，近几十年来一直是人们重新关注的焦点。为了指导未来的育种和作物改良工作，该社区需要更深入地理解亚基因组优势，这通常在同种异体多倍体物种中引起，同时需要了解育种计划中存在的材料的遗传多样性和种群结构。我们利用新基因组对 C. sativa 多样性面板进行了种群遗传分析，以估计核苷酸多样性和种群结构，并分析了不同器官之间亚基因组表达优势的模式。我们的分析证实 C. sativa 具有相对较低的遗传多样性，并表明与其他两个亚基因组相比，SG3 亚基因组的遗传多样性要低得多。尽管遗传多样性较低，但我们的分析确定了 13 个不同的亚种群，包括两个不同的野生种群和其他推定代表现有育种种群中的创始人的亚种群。在分析已知在 （a） 生物胁迫耐受性中起重要作用的长链非编码 RNA 的亚基因组组成时，我们发现与其他亚基因组相比，SG3 亚基因组包含的 lincRNA 明显更多。同样，转录组分析显示 SG3 的表达显性并不像以前报道的那样强，并且可能不是在所有器官类型中都普遍存在。从整体分析来看，SG3 仅在花、花芽和果器官中的表达量显著升高，鉴于作物产量与这些器官相关，这是一项重要的发现。总的来说，这些结果对于指导未来的山茶花育种工作很有价值。