Transcriptional Dynamics and Candidate Genes Involved in Pod Maturation of Common Bean (Phaseolus vulgaris L.)

Abstract

Pod maturation of common bean relies upon complex gene expression changes, which in turn are crucial for seed formation and dispersal. Hence, dissecting the transcriptional regulation of pod maturation would be of great significance for breeding programs. In this study, a comprehensive characterization of expression changes has been performed in two common bean cultivars (ancient and modern) by analyzing the transcriptomes of five developmental pod stages, from fruit setting to maturation. RNA-seq analysis allowed for the identification of key genes shared by both accessions, which in turn were homologous to known Arabidopsis maturation genes and furthermore showed a similar expression pattern along the maturation process. Gene-expression changes suggested a role in promoting an accelerated breakdown of photosynthetic and ribosomal machinery associated with chlorophyll degradation and early activation of alpha-linolenic acid metabolism. A further study of transcription factors and their DNA binding sites revealed three candidate genes whose functions may play a dominant role in regulating pod maturation. Altogether, this research identifies the first maturation gene set reported in common bean so far and contributes to a better understanding of the dynamic mechanisms of pod maturation, providing potentially useful information for genomic-assisted breeding of common bean yield and pod quality attributes.Plants 2020, 9, 545 2 of 20 metabolites such as carotenoids and anthocyanins [7][8][9][10][11]. Likewise, jasmonate promotes senescence and plays an important role in chlorophyll degradation [12,13], which is synthesized from alpha-linolenic acid [14,15], suggesting that the accumulation of this acid during maturation is responsible for stimulating chlorophyll loss [16]. In addition, the increased accumulation of antioxidant and monoterpene is also an important feature of the fruit maturation process [17][18][19].Like most species of the Fabaceae (also named as Leguminosae) family, common bean (Phaseolus vulgaris L.) produces dry fruits in the form of a pod, which is a photosynthetically active organ that encloses the developing seeds and protects them from pests and pathogens. Indeed, photosynthetically active pod tissue contributes to fuel seed growth with assimilates and nutrients [20]. As in most angiosperms, significant genetic, biochemical, and physiological changes take place during fruit maturation, which confers the functional and morphological properties of this plant organ. Unlike members of the Brassicaceae family that produce pods (siliques) derived from two fused carpels, legume pods are developed from a single carpel that emerges from the gynoecium after ovule fertilization. Subsequently, pods attain their maximum size through a growth phase caused by an active cell division and later cell expansion [21]. During the maturation phase, carbohydrate metabolism and amino acid biosynthesis are increased in pods, leading to the accumulation of storage compounds, mainly starch, total soluble amino acids, an...

GWAS of pod morphological and color characters in common bean

“…Five of these candidate genes were Cytochrome P450 and five were WRKY or MYB transcription factors, proteins involved in multiple processes like responses to biotic and abiotic stresses, development, differentiation, metabolism, defense, and pigment synthesis [ 23 , 24 ]. Seven of these genes were involved in controlling pod development: Phvul.001G229900, Phvul.001G221500, Phvul.002G016100, Phvul.004G144900, Phvul.006G076800, Phvul.006G077200 and Phvul.010G010200 [ 25 ]. Four genes, homologous with genes controlling silique size in A. thalina [ 26 ] were detected underlying QTL associated with both size and color traits: Phvul.001G262600 with SPL10 gene in QTL NSPCol01_51; Phvul.002G141800 with FIS2 gene near QTL PodL02_29.1; Phvul.006G074600 with TTG2 gene in QTLPodLSN06_18.4; and Phvul.008G019500 with AML4 gene in QTL NSPCol08_1.7.…”

Single and multi‐trait genome‐wide association studies identify genomic regions associated with phenological traits in cowpea

“…For example, we found genes involved in phosphorylation ( VuUCR779.09G005600 ; VuUCR779.05G102400 ), which plays important roles in a variety of critical processes in plants such as metabolism, regulation of photosystem, and circadian system (Cheng et al., 2014). Interestingly, a previous study concluded that phosphorylation acts as an important regulatory mechanism for the expression of pod maturity in common beans (Gómez‐Martín et al., 2020). In addition, this same study found that fatty acid biosynthesis, also identified in our study ( VuUCR779.09G005500 ), is relevant for the maturation process, also corroborating with studies with other species (Simpson et al., 2016; Zhang et al., 2016).…”

“…In addition, this same study found that fatty acid biosynthesis, also identified in our study ( VuUCR779.09G005500 ), is relevant for the maturation process, also corroborating with studies with other species (Simpson et al., 2016; Zhang et al., 2016). We also identified genes related to the regulation of DNA‐templated transcription ( VuUCR779.03G017100 ; VuUCR779.09G060000 ; and VuUCR779.07G116400 ) for all the assessed traits, including PC1, which has also been described as involved in the pod maturation process in common bean (Gómez‐Martín et al., 2020) and peanut (Wu et al., 2022).…”

GWAS Of Pod Morphological and Color Characters in Common Bean

“…Five of these candidate genes were Cytochrome P450 and ve were WRKY or MYB transcription factors, proteins involved in multiple processes like responses to biotic and abiotic stresses, development, differentiation, metabolism, defense, and pigment synthesis [23,24]. Seven of these genes were involved in controlling pod development: Phvul.001G229900, Phvul.001G221500, Phvul.002G016100, Phvul.004G144900, Phvul.006G076800, Phvul.006G077200 and Phvul.010G010200 [25]. Four genes, homologous with genes controlling silique size in A. thalina [26] were detected underlying QTL associated with both size and color traits: Phvul.001G262600 with SPL10 gene in QTL NSPCol01_51; Phvul.002G141800 with FIS2 gene near QTL PodL02_29.1; Phvul.006G074600 with TTG2 gene in QTLPodLSN06_18.4; and Phvul.008G019500 with AML4 gene in QTL NSPCol08_1.7.…”