sj-pdf-1-ajs-10.1177_03635465231194028 – Supplemental material for Meniscal Fibrocartilage Repair Based on Developmental Characteristics

Supplemental material, sj-pdf-1-ajs-10.1177_03635465231194028 for Meniscal Fibrocartilage Repair Based on Developmental Characteristics by Wenqiang Yan, Jingxian Zhu, Yue Wu, Yiqun Wang, Cancan Du, Jin Cheng, Xiaoqing Hu and Yingfang Ao in The American Journal of Sports Medicine</p

Combined bulked segregant sequencing and traditional linkage analysis for identification of candidate gene for purple leaf sheath in maize

<div><p>Anthocyanin accumulation in various maize tissues plays important roles in plant growth and development. In addition, some color-related traits can be used as morphological markers in conventional maize breeding processes and purity identification of hybrid seeds. Here, we noticed that the leaf sheath color was controlled by a dominant gene, because purple (PSH) and green leaf sheaths (GSH) were separated at a ratio of 3:1 in an F₂ population. To map the gene, an F₂ and a recombinant inbred line (RIL) population were derived from a cross between inbred line T877 (PSH) and DH1M (GSH). The <i>PSH</i> locus was mapped to the genomic region within 128.8 to 138.4 Mb using a bulked segregant sequencing approach. This position was further validated by linkage mapping using 190 F₂ plants with GSH. Subsequently, the <i>PSH</i> locus was fine-mapped into an interval of 304.2 kb. A maize gene, GRMZM5G822829, was identified in this region, encoding a bHLH transcription factor. The expression level of this gene in T877 was found to be 9-fold higher than that of DH1M. In conclusion, our results suggest that GRMZM5G822829 is the putative candidate gene conferring leaf sheath color in maize.</p></div

The relative expression levels of <i>PSH</i> in different tissues for T877 and DH1M.

<p>Root1 and root2 indicated roots exposed to light and in the dark, respectively. The lowercase letters “a” indicate that the gene is almost non-expressed, “**” indicate that a significant difference was detected between T877 and DH1M in the same tissue sample (<i>p</i><0.01).</p

Candidate genes in <i>PSH</i> region.

<p>Candidate genes in <i>PSH</i> region.</p

Statistics of sequencing depth and coverage.

<p>Statistics of sequencing depth and coverage.</p

Isolation and sequence analysis of the gene conferring responsible for purple leaf sheath.

<p>(a) Fine mapping the <i>PSH</i> locus to the region between markers IDP7541 and TIDP5239. (b) Fine mapping narrows down the <i>PSH</i> locus to 304.2 kb between markers Indel02A and Indel01C. (c) The predicted genes in the 304.2 kb genomic region. (d) Gene structure of <i>PSH</i> and sequence analysis of T877 and DH1M.</p

DNA chip screening across 190 F₂ plants mapped the <i>PSH</i> locus onto chromosome 10.

<p>The black dashed line represents the 5% significance threshold with a Bonferroni correction.</p

SNPs significantly associated with purple leaf sheath (PSH).

<p>SNPs significantly associated with purple leaf sheath (PSH).</p

Single nucleotide polymorphism (SNP)-index plots across the whole genome (a) and chromosome 10 (b).

<p>Single nucleotide polymorphism (SNP)-index plots across the whole genome (a) and chromosome 10 (b).</p

Phenotypes of parental inbred lines (a) and progeny lines in RIL population (b) in sixth leaf stage.

<p>Phenotypes of parental inbred lines (a) and progeny lines in RIL population (b) in sixth leaf stage.</p