The Identification Of Long-InDel Variation For Fine Mapping Of QPH16 Locus Controlling Plant Height In Soybean

Soybean(Glycine max L.Merr.)is one of the most important economic crops in the world which is also the main source of plant protein and plant oil.Plant height is one of the important agronomic traits closely related to soybean yield.Studies have shown that fine mapping or map based cloning of quantitative trait locus(QTL)or genes controlling plant height can significantly improve plant height by molecular breeding methods such as gene editing or marker assisted selection.Insertion-Deletion(InDel)is the most common genetic variation compared to single nucleotide polymorphism(SNP).In previous studies,the longInDel(> 15bp)of soybean was not studied comprehensively and deeply.In this study,soybean varieties Zhong Pin03-5373 and Zhong Huang13 were used as experimental materials,and the whole genome re-sequencing technology was used to explore the long-InDel variation and clarify the variation characteristics,and the long-InDel markers was developed to fine map the QTL qPH16 related to plant height initially located in the recombinant inbred line population derived from Zhong Pin03-5373 and Zhong Huang13,It can provide more comprehensive genetic variation information for genetic analysis and molecular assisted selection breeding of soybean important agronomic traits.The key research findings were as followed:(1)Through the whole genome re-sequencing of soybean lines/varieties Zhong Pin03-5373 and Zhong Huang13,13573 InDels with the length of 16-53 bp were detected.There was a significant negative correlation between the length and the number of InDels,and they were unevenly distributed on 20 chromosomes of soybean,and the average density of chromosome arm region was significantly higher than that of pericentromeric region.(2)GO annotation analysis of large effect InDel(leading in truncation or extension of coding amino acids)using AgriGO software found that 319 long-InDels were significantly enriched in the ADP binding term,rich in 14 resistance-related genes.(3)In order to further use long-InDels for genetic analysis of soybean,we focused on a previously reported QTL locus qPH16 for plant height.All the 35 long-InDels variation sites detected in the mapping interval of qPH16 were developed into InDel markers.A total of 26markers(74.3%)showed significant polymorphism among parents.The genomic region of qPH16 was narrowed from 960 kb to 477.55 kb.(4)Based on the large effect SNP and InDel detected in qPH16 locus,combined with RNA-Seq data and homologous gene function analysis in Arabidopsis,we selected Glyma.16G163800 as a candidate gene for QTL qPH6 locus.To sum up,the plant height related qPH16 locus were successfully mapped from 960 kb down to 477.55 kb by identifying long-InDel mutations and developing long-InDel markers through whole genome re-sequencing technology in this study.