Elimination of an unfavorable allele conferring pod shattering in an elite soybean cultivar by CRISPR/Cas9

Zhihui Zhang; Jie Wang; Huaqin Kuang; Zhihong Hou; Pingping Gong; Mengyan Bai; Shaodong Zhou; Xiaolei Yao; Shikui Song; Long Yan; Yuefeng Guan

doi:10.1007/s42994-022-00071-8

Elimination of an unfavorable allele conferring pod shattering in an elite soybean cultivar by CRISPR/Cas9

aBIOTECH. 2022 Mar 7;3(2):110-114. doi: 10.1007/s42994-022-00071-8. eCollection 2022 Jun.

Authors

Zhihui Zhang^#¹, Jie Wang^#^{1

2}, Huaqin Kuang^#², Zhihong Hou^#³, Pingping Gong², Mengyan Bai⁴, Shaodong Zhou¹, Xiaolei Yao¹, Shikui Song², Long Yan⁵, Yuefeng Guan²

Affiliations

¹ College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China.
² FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China.
³ College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319 Heilongjiang China.
⁴ College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China.
⁵ The Key Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035 China.

^# Contributed equally.

Abstract

Pod shattering can lead to devastating yield loss of soybean and has been a negatively selected trait in soybean domestication and breeding. Nevertheless, a significant portion of soybean cultivars are still pod shattering-susceptible, limiting their regional and climatic adaptabilities. Here we performed genetic diagnosis on the shattering-susceptible trait of a national registered cultivar, Huachun6 (HC6), and found that HC6 carries the susceptible genotype of a candidate Pod dehiscence 1 (PDH1) gene, which exists in a significant portion of soybean cultivars. We next performed genome editing on PDH1 gene by clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9). In T₂ progenies, several transgene-free lines with pdh1 mutations were characterized without affecting major agronomic traits. The pdh1 mutation significantly improved the pod shattering resistance which is associated with aberrant lignin distribution in inner sclerenchyma. Our work demonstrated that precision breeding by genome editing on PDH1 holds great potential for precisely improving pod shattering resistance and adaptability of soybean cultivars.

Keywords: CRISPR/Cas9; Genome editing; Marker assisted selection; Pod shattering; Precision breeding; Soybean.