Understandings and future challenges in soybean functional genomics and molecular breeding

Abstract

Soybean (Glycine max) is a major source of plant protein and oil. Soybean breeding has benefited from advances in functional genomics. In particular, the release of soybean reference genomes has advanced our understanding of soybean adaptation to soil nutrient deficiencies, the molecular mechanism of symbiotic nitrogen (N) fixation, biotic and abiotic stress tolerance, and the roles of flowering time in regional adaptation, plant architecture, and seed yield and quality. Nevertheless, many challenges remain for soybean functional genomics and molecular breeding, mainly related to improving grain yield through high‐density planting, maize–soybean intercropping, taking advantage of wild resources, utilization of heterosis, genomic prediction and selection breeding, and precise breeding through genome editing. This review summarizes the current progress in soybean functional genomics and directs future challenges for molecular breeding of soybean.

Effects of exogenous calcium and calcium inhibitor on physiological characteristics of winter rape (Brassica rapa) under low temperature stress

“…All of these processes are fundamental to the cell's life activities and are essential for its proper functioning. Calmodulin is an important intracellular signaling protein that binds to calcium ions in response to cellular stimuli, thereby regulating cellular biological responses [53] . Changes in the expression levels of these genes can have signi cant effects on plant growth, cell signaling, and transmembrane transport, and may represent cellular responses to maintain normal life activities in the face of environmental stress or challenge [54] .…”

Origin, variation, and selection of natural alleles controlling flowering and adaptation in wild and cultivated soybean

“…In soybean, the classical maturity loci E1 to E11 , the LJ locus J , FLOWERING TIME 2a ( FT2a , also named LJ16.1 ), FT5a (also named LJ16.2 ), and several other QTLs including Time of Flowering 4 ( Tof4 ), Tof5 , Tof11 (also named Growth period 11 [ Gp11 ]), Tof12 (also named Gp12/qFT12-1 ), Tof16 , Tof18 , and QTL near E1 ( QNE1 ) have been identified in segregating populations derived from crosses between cultivars with contrasting phenotypes (Bernard 1971 ; Buzzell 1971 ; Buzzell and Voldeng 1980 ; McBlain and Bernard 1987 ; Bonato and Vello 1999 ; Cober and Voldeng 2001 ; Cober et al 2010 ; Kong et al 2014 ; Samanfar et al 2017 ; Wang et al 2019 ; Ray et al 1995 ; Dong et al 2021 , 2022a , 2023 ; Lu et al 2017 , 2020 ; Li et al 2021 ; Kou et al 2022 ; Xia et al 2022 ). The dominant alleles of E1 , E2 (as homologue of GIGANTEA [ GIa ]), E3 (homologue of PHYTOCHROME A3 , PHYA3 ), E4 ( PHYA2 ), E7 , E8 , E10 (also named FT4 ), Tof4 ( E1 like 1a, E1la ), Tof11 ( PSEUDO-RESPONSE REGULATOR 3a , PRR3a ), and Tof12 ( PRR3b ) delay flowering, whereas the dominant alleles of E6/J ( EARLY FLOWERING 3 , ELF3 ), E9 (also named LJ16.1 , FT2a ), E11 , LJ16.2 ( FT5a ), Tof5 ( FRUITFULL 2a , FUL2a ), Tof16 ( LATE ELONGATED HYPOCOTYL 1a , LHY1a ), Tof18 ( SUPPRESSOR OF OVEREXPRESSION OF CO 1a , SOC1a ), and QNE1 promote flowering (Dong et al 2023 ; Du et al 2023 ; Hou et al 2022 ; Lin et al 2021a , 2021b , 2022; Wang et al 2023a , 2023b ). Besides the above loci/genes, some other important genes have been characterized through reverse-genetic approaches and have been shown to be involved in the photoperiodic control of flowering time, such as the circadian clock genes LUX ARRYTHMO ( LUX1 ) and LUX2 (Bu et al 2021 ) and NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED 2 ( LNK2 ) (Li et al 2020b ), CONSTANS-like ( COL1a , COL1b ...…”

“…Unlike the model species Arabidopsis ( Arabidopsis thaliana ) (Shim et al 2017 ), the photoperiod flowering pathways in soybean is centered on the legume-specific B3-like transcriptional repressor E1 (Xia et al 2012 ; Xu et al 2015 ). E1 integrates upstream light receptors (E3 and E4) and circadian clock (E2, J, LUX1, LUX2, Tof11, Tof12, and Tof16) signals to downstream genes to control photoperiodic flowering (Du et al 2023 ; Hou et al 2022 ; Lin et al 2021b ). Tof11 and Tof12 promote E1 expression by repressing the circadian clock gene LHY under long-day conditions (Lu et al 2020 ).…”

“…As the central hub in soybean photoperiod flowering, E1 then transfers these signals to the florigen genes FT s as output (Du et al 2023 ; Hou et al 2022 ; Lin et al 2021b ). E1 confers late flowering, mainly by inhibiting the expression of FT2a and FT5a (Kong et al 2010 ; Nan et al 2014 ; Thakare et al 2011 ; Xia et al 2012 ; Xu et al 2015 ), as well as inducing the expression of the flowering repressor genes FT1a and FT4 (Zhai et al 2014 ).…”

“…The wide distribution of cultivated soybean and its wild ancestors is controlled by many maturity genes, as reflected by quantitative trait loci (QTLs) controlling photoperiodic flowering and maturity. Several major flowering and maturity loci have been identified and functionally characterized in soybean, including maturity genes, long-juvenile (LJ) genes, and several QTLs (Lin et al 2021a , 2021b ; Hou et al 2022 ; Du et al 2023 ; Liang and Tian 2023 ; Wang et al 2023a ). Variations or natural alleles of these genes or QTLs controlling photoperiodic flowering and maturation have been artificially or naturally selected at different latitudes, allowing soybean to adapt to wide latitudes.…”