Systematic Analysis of BELL Family Genes in Zizania latifolia and Functional Identification of ZlqSH1a/b in Rice Seed Shattering

Abstract

The loss of seed shattering is an important event in crop domestication, and elucidating the genetic mechanisms underlying seed shattering can help reduce yield loss during crop production. This study is the first to systematically identify and analyse the BELL family of transcription factor-encoding genes in Chinese wild rice (Zizania latifolia). ZlqSH1a (Zla04G033720) and ZlqSH1b (Zla02G027130) were identified as key candidate genes involved in seed shattering in Z. latifolia. These genes were involved in regulating the development of the abscission layer (AL) and were located in the nucleus of the cell. Over-expression of ZlqSH1a and ZlqSH1b resulted in a complete AL between the grain and pedicel and significantly enhanced seed shattering after grain maturation in rice. Transcriptome sequencing revealed that 172 genes were differentially expressed between the wild type (WT) and the two transgenic (ZlqSH1a and ZlqSH1b over-expressing) plants. Three of the differentially expressed genes related to seed shattering were validated using qRT-PCR analysis. These results indicate that ZlqSH1a and ZlqSH1b are involved in AL development in rice grains, thereby regulating seed shattering. Our results could facilitate the genetic improvement of seed-shattering behaviour in Z. latifolia and other cereal crops.

Genome‐wide analysis, metabolomics, and transcriptomics reveal the molecular basis of ZlRc overexpression in promoting phenolic compound accumulation in rice seeds

“…The sources of Escherichia coli DH5α‐competent cells, T‐vector, 1390‐UBI overexpression vector, and pEGOEP35S‐H‐green fluorescent protein (GFP) overexpression vector were described by Xie et al. (2022).…”

“…The Z. latifolia bHLH gene‐family was identified according to the methods of Xie et al. (2022). The MapGene2Choromosome v2.0 online tool was used for the chromosome location analysis of ZlbHLH family genes.…”

“…ZlRc amplification, transformation, and sequencing were performed according to the methods of Xie et al. (2022). ZlRc‐F and ZlRc‐R primers are shown in Table S1.…”

“…The Agrobacterium-mediated transformation of rice (O. sativa cv. Nipponbare) and identification of OE rice plants were performed according to the methods of Xie et al (2022). Pictures from the agarose electrophoresis of positive transgenic rice plants are shown in Figure S2.…”

Domestication, breeding, omics research, and important genes of Zizania latifolia and Zizania palustris

“…In particular, it is rich in protein, essential amino acids, fatty acids, vitamins, and microelements ( Yan et al., 2018 ). Due to its high nutritional value, developing germplasms resistant to seed shattering remains a top priority in the domestication and breeding of Z. latifolia ( Xie et al., 2022 ). As a graminaceous crop closely related to rice, Z. latifolia boasts myriad beneficial traits that rice lacks, including rice blast resistance, thick stalks, strong tillering, low-temperature resistance, flood resistance, rapid grouting maturity, high biological yields, and optimizing protein and lysine contents in seeds ( Chen et al., 2012 ; Ye et al., 2016 ; Yan et al., 2022 ).…”