Table_4_Construction of High-Density Genetic Maps and Detection of QTLs Associated With Huanglongbing Tolerance in Citrus.docx

Huanglongbing (HLB), or citrus greening, is the most devastating disease in citrus worldwide. Commercial citrus varieties including sweet orange (Citrus sinensis) are highly susceptible to HLB, and trifoliate orange (Poncirus trifoliata, a close Citrus relative) is widely considered resistant or highly tolerant to HLB. In this study, an intergeneric F1 population of sweet orange and trifoliate orange was genotyped by Genotyping-by-Sequencing, and high-density SNP-based genetic maps were constructed separately for trifoliate orange and sweet orange. The two genetic maps exhibited high synteny and high coverage of the citrus genome. Progenies of the F1 population and their parents were planted in a replicated field trial, exposed to intense HLB pressure for 3 years, and then evaluated for susceptibility to HLB over 2 years. The F1 population exhibited a wide range in severity of HLB foliar symptom and canopy damage. Genome-wide QTL analysis based on the phenotypic data of foliar symptom and canopy damage in 2 years identified three clusters of repeatable QTLs in trifoliate orange linkage groups LG-t6, LG-t8 and LG-t9. Co-localization of QTLs for two traits was observed within all three regions. Additionally, one cluster of QTLs in sweet orange (linkage group LG-s7) was also detected. The majority of the identified QTLs each explained 18–30% of the phenotypic variation, indicating their major role in determining HLB responses. These results show, for the first time, a quantitative genetic nature yet the presence of major loci for the HLB tolerance in trifoliate orange. The results suggest that sweet orange also contains useful genetic factor(s) for improving HLB tolerance in commercial citrus varieties. Findings from this study should be very valuable and timely to researchers worldwide as they are hastily searching for genetic solutions to the devastating HLB crisis through breeding, genetic engineering, or genome editing.

黄龙病（HLB），亦称柑橘衰退病，是全球柑橘类作物最致命的病害。包括甜橙（Citrus sinensis）在内的商业柑橘品种对HLB高度易感，而三叶橙（Poncirus trifoliata，与柑橘属密切相关的物种）则普遍被认为对HLB具有抵抗力或高度耐受性。在本研究中，通过对甜橙和三叶橙的杂交F1群体进行基因分型测序，分别构建了三叶橙和甜橙的高密度SNP基遗传图谱。这两个遗传图谱在柑橘基因组中表现出高度的连锁一致性和广泛的覆盖范围。F1群体的后代及其亲本在重复的田间试验中种植，暴露于强烈的HLB压力下3年，随后在接下来的2年内对其对HLB的易感性进行了评估。F1群体在HLB叶片症状和树冠损伤的严重程度上表现出广泛的变异。基于F1群体两年内叶片症状和树冠损伤表型的全基因组QTL分析，在三叶橙的连锁群LG-t6、LG-t8和LG-t9中识别出三个可重复的QTL簇。在所有三个区域均观察到两个性状QTL的共定位。此外，在甜橙（连锁群LG-s7）中亦检测到一个QTL簇。大多数已识别的QTL解释了18-30%的表型变异，表明它们在决定HLB反应中的主要作用。这些结果首次揭示了三叶橙HLB耐受性存在的主要基因位点，并具有数量遗传性质。研究结果提示，甜橙亦含有对提高商业柑橘品种HLB耐受性有用的遗传因子。本研究的结果对于全球研究人员而言极具价值和时效性，因为他们正急于通过育种、基因工程或基因组编辑等途径寻找解决HLB灾难性危机的遗传解决方案。