Mi Qi, Pang Hongqian, Luan Feishi, Gao Peng, Liu Shi
Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, Heilongjiang Province, China.
College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, Heilongjiang Province, China.
Theor Appl Genet. 2023 Apr 4;136(4):95. doi: 10.1007/s00122-023-04320-2.
The scc locus of the watermelon seed coat crack trait was fine mapped on chromosome 3. Cla97C03G056110 (annotated as CRIB domain-containing protein) was regarded as the most likely candidate gene Seed coat crack (scc) is a special characteristic of watermelon compared with other cucurbit crops. However, information regarding the genetic basis of this trait is limited. We conducted a genetic analysis of six generations derived from PI 192938 (scc) and Cream of Saskatchewan (COS) (non-scc) parental lines and found that the scc trait was regulated by a single recessive gene through two years. Bulk segregant analysis sequencing (BSA-seq) and initial mapping placed the scc locus into an 808.8 kb region on chromosome 3. Evaluation of another 1152 F plants narrowed the scc locus to a 277.11 kb region containing 37 candidate genes. Due to the lack of molecular markers in the fine-mapping interval, we extracted the genome sequence variations in this 277.11 kb region with in silico BSA among seventeen re-sequenced lines (6 scc and 11 non-scc) and finally delimited the scc locus to an 8.34 kb region with only one candidate gene Cla97C03G056110 (CRIB domain-containing protein). Three single nucleotide polymorphism loci in the promoter region of Cla97C03G056110 altered cis-acting elements that were highly correlated with the nature watermelon panel. The expression of Cla97C03G056110 in seed coat tissue was higher in non-scc than in scc lines and was specifically expressed in seed coat compared with fruit flesh.
西瓜种皮开裂性状的scc基因座在3号染色体上被精细定位。Cla97C03G056110（注释为含CRIB结构域的蛋白）被认为是最有可能的候选基因。与其他葫芦科作物相比，种皮开裂（scc）是西瓜的一个特殊特征。然而，关于该性状遗传基础的信息有限。我们对来自PI 192938（scc）和萨斯喀彻温奶油瓜（COS）（非scc）亲本系的六代进行了遗传分析，发现经过两年时间，scc性状由一个单隐性基因调控。混合分组分析法测序（BSA-seq）和初步定位将scc基因座定位到3号染色体上一个808.8 kb的区域。对另外1152株F植株的评估将scc基因座缩小到一个包含37个候选基因的277.11 kb区域。由于精细定位区间缺乏分子标记，我们通过对17个重测序品系（6个scc和11个非scc）进行电子混合分组分析法，提取了这个277.11 kb区域的基因组序列变异，最终将scc基因座限定到一个仅包含一个候选基因Cla97C03G056110（含CRIB结构域的蛋白）的8.34 kb区域。Cla97C03G056110启动子区域的三个单核苷酸多态性位点改变了顺式作用元件，这些元件与自然西瓜群体高度相关。Cla97C03G056110在非scc品系种皮组织中的表达高于scc品系，并且与果肉相比，在种皮中特异性表达。
