AUTHOR=Liu Lü-Meng , Zhang Han-Qing , Cheng Kun , Zhang Yuan-Ming 

TITLE=Integrated Bioinformatics Analyses of PIN1, CKX, and Yield-Related Genes Reveals the Molecular Mechanisms for the Difference of Seed Number Per Pod Between Soybean and Cowpea

JOURNAL=Frontiers in Plant Science

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2021.749902

DOI=10.3389/fpls.2021.749902

ISSN=1664-462X

ABSTRACT=<p>There is limited advancement on seed number per pod (SNPP) in soybean breeding, resulting in low yield in China. To address this issue, we identified <italic>PIN1</italic> and <italic>CKX</italic> gene families that regulate SNPP in <italic>Arabidopsis</italic>, analyzed the differences of auxin and cytokinin pathways, and constructed interaction networks on <italic>PIN1, CKX</italic>, and yield-related genes in soybean and cowpea. First, the relative expression level (REL) of <italic>PIN1</italic> and the plasma membrane localization and phosphorylation levels of PIN1 protein were less in soybean than in cowpea, which make auxin transport efficiency lower in soybean, and its two interacted proteins might be involved in serine hydrolysis, so soybean has lower SNPP than cowpea. Then, the <italic>CKX</italic> gene family, along with its positive regulatory factor <italic>ROCK1</italic>, had higher REL and less miRNA regulation in soybean flowers than in cowpea ones. These lead to higher cytokinin degradation level, which further reduces the REL of <italic>PIN1</italic> and decreases soybean SNPP. We found that <italic>VuACX4</italic> had much higher REL than <italic>GmACX4</italic>, although the two genes essential in embryo development interact with the <italic>CKX</italic> gene family. Next, a tandem duplication experienced by legumes led to the differentiation of <italic>CKX3</italic> into <italic>CKX3a</italic> and <italic>CKX3b</italic>, in which <italic>CKX3a</italic> is a key gene affecting ovule number. Finally, in the yield-related gene networks, three cowpea <italic>CBP</italic> genes had higher RELs than two soybean <italic>CBP</italic> genes, low RELs of three soybean-specific <italic>IPT</italic> genes might lead to a decrease in cytokinin synthesis, and some negative and positive SNPP regulation were found, respectively, in soybean and cowpea. These networks may explain the SNPP difference in the two crops. We deduced that <italic>ckx3a</italic> or <italic>ckx3a ckx6 ckx7</italic> mutants, interfering <italic>CYP88A</italic>, and over-expressed <italic>DELLA</italic> increase SNPP in soybean. This study reveals the molecular mechanism for the SNPP difference in the two crops, and provides an important idea for increasing soybean yield.</p>