Factors Influencing the Emergence of Heterogeneous Populations of Common Bean (Phaseolus vulgaris L.) and Their Potential for Intercropping

The common bean is an important legume valued for its protein-rich seeds and its ability to fix nitrogen, making it a key element of crop rotation. In conventional agriculture, the emphasis is on uniformity and genetic purity to optimize crop performance and maximize yields. This is due to both the legal obligations to register varieties and the challenges of implementing breeding programs to create genetically diverse varieties. This paper focuses on the factors that influence the occurrence of heterogeneous common bean populations. The main factors contributing to this diversity have been described, including local adaptations, variable weather conditions, different pollinator species, and intricate interactions between genes controlling seed coat colour. We also discuss the benefits of intercropping common beans for organic farming systems, highlighting the improvement in resistance to diseases, and adverse environmental conditions. This paper contributes to a better understanding of common bean seed heterogeneity and the legal obligation to use heterogeneous populations.

Chromosome-level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean

Adzuki bean (Vigna angularis) is an important legume crop cultivated in over 30 countries worldwide. We developed a high-quality chromosome-level reference genome of adzuki bean cultivar Jingnong6 by combining PacBio Sequel long-read sequencing with short-read and Hi-C technologies. The assembled genome covers 97.8% of the adzuki bean genome with a contig N50 of approximately 16 Mb and a total of 32 738 protein-coding genes. We also generated a comprehensive genome variation map of adzuki bean by whole-genome resequencing (WGRS) of 322 diverse adzuki beans accessions including both wild and cultivated. Furthermore, we have conducted comparative genomics and a genome-wide association study (GWAS) on key agricultural traits to investigate the evolution and domestication. GWAS identified several candidate genes, including VaCycA3;1, VaHB15, VaANR1 and VaBm, that exhibited significant associations with domestication traits. Furthermore, we conducted functional analyses on the roles of VaANR1 and VaBm in regulating seed coat colour. We provided evidence for the highest genetic diversity of wild adzuki (Vigna angularis var. nipponensis) in China with the presence of the most original wild adzuki bean, and the occurrence of domestication process facilitating transition from wild to cultigen. The present study elucidates the genetic basis of adzuki bean domestication traits and provides crucial genomic resources to support future breeding efforts in adzuki bean.

and Coss.] is associated with Bju.TT8 homologs identifiable by targeted functional markers

Seed coat colour is an important trait in Indian mustard. Breeding for seed coat colour needs precise knowledge of mode of inheritance and markers linked to it. The present study was focussed on genetics and development of functional markers for seed coat colour. F₁s (direct and reciprocal) and F₂ populations were developed by crossing two contrasting parents for seed coat colour (DRMRIJ-31, brown seeded and RLC-3, yellow seeded). Phenotypic results have shown that the seed coat colour trait was under the influence of maternal effect and controlled by digenic-duplicate gene action. Further, Bju.TT8 homologs of both parents (DRMRIJ-31 and RLC-3) were cloned and sequenced. Sequencing results of Bju.TT8 homologs revealed that in RLC-3, gene Bju.ATT8 had an insertion of 1279bp in the 7^th exon; whereas, gene Bju.BTT8 had an SNP (C→T) in the 7^th exon. These two mutations were found to be associated with yellow seed coat colour. Using sequence information, functional markers were developed for both Bju.TT8 homologs, validated on F₂ population and were found highly reliable with no recombination between the markers and the phenotype. Further, these markers were subjected to a germplasm assembly of Indian mustard, and their allelic combination for the seed coat colour genes has been elucidated. The comparative genomics of TT8 genes revealed high degree of similarity between and across the Brassica species, and the respective diploid progenitors in tetraploid Brassica species are the possible donors of TT8 homologs. This study will help in the marker-assisted breeding for seed coat colour, and aid in understanding seed coat colour genetics more precisely.

VaSDC1 Is Involved in Modulation of Flavonoid Metabolic Pathways in Black and Red Seed Coats in Adzuki Bean (Vigna angularis L.)

Seed coat colour is an important nutritional quality trait. Variations in anthocyanins and flavonoids induce the diversity of seed coat colour in adzuki bean (Vigna angularis L.). Red seed coat and black seed coat are important adzuki bean cultivars. Insights into the differences of flavonoid metabolic pathways between black and red adzuki bean are significant. In this study, we explored that the difference in seed coat colour between the red (Jingnong6) and the black (AG118) is caused by the accumulation of anthocyanins. The RNA-sequencing (RNA-Seq) and real-time reverse transcription (qRT)-PCR results showed that the Vigna angularis L. seed coat color (VaSDC1) gene, an R2R3-MYB transcription factor, should be the key gene to regulate the black and red seed coat colours. In three different colouring staes of seed development, VaSDC1 was specifically expressed in the black seed coat (AG118) landrace, which activates the structural genes of flavonoid metabolic pathways. As a result, this caused a substantial accumulation of anthocyanins and created a dark blue-black colour. In the red (Jingnong6) seed coat variety, low expression levels of VaSDC1 resulted in a lower accumulation of anthocyanins than in AG118. In addition, VaSDC1 was genetically mapped in the interval between simple-sequence repeat (SSR) markers Sca326-12, Sca326-4, and BAgs007 on chromosome 3 using an F₄ segregating population derived from the cross between Jingnong6 and AG118. These results will facilitate the improvement of nutritional quality breeding in adzuki beans.

Targeted mutagenesis of BnTT8 homologs controls yellow seed coat development for effective oil production in Brassica napus L

Yellow seed is a desirable trait with great potential for improving seed quality in Brassica crops. Unfortunately, no natural or induced yellow seed germplasms have been found in Brassica napus, an important oil crop, which likely reflects its genome complexity and the difficulty of the simultaneous random mutagenesis of multiple gene copies with functional redundancy. Here, we demonstrate the first application of CRISPR/Cas9 for creating yellow-seeded mutants in rapeseed. The targeted mutations of the BnTT8 gene were stably transmitted to successive generations, and a range of homozygous mutants with loss-of-function alleles of the target genes were obtained for phenotyping. The yellow-seeded phenotype could be recovered only in targeted mutants of both BnTT8 functional copies, indicating that the redundant roles of BnA09.TT8 and BnC09.TT8b are vital for seed colour. The BnTT8 double mutants produced seeds with elevated seed oil and protein content and altered fatty acid (FA) composition without any serious defects in the yield-related traits, making it a valuable resource for rapeseed breeding programmes. Chemical staining and histological analysis showed that the targeted mutations of BnTT8 completely blocked the proanthocyanidin (PA)-specific deposition in the seed coat. Further, transcriptomic profiling revealed that the targeted mutations of BnTT8 resulted in the broad suppression of phenylpropanoid/flavonoid biosynthesis genes, which indicated a much more complex molecular mechanism underlying seed colour formation in rapeseed than in Arabidopsis and other Brassica species. In addition, gene expression analysis revealed the possible mechanism through which BnTT8 altered the oil content and fatty acid composition in seeds.

Identification of candidate genes for the seed coat colour change in a Brachypodium distachyon mutant induced by gamma radiation using whole-genome re-sequencing

Brachypodium distachyon has been proposed as a model plant for agriculturally important cereal crops such as wheat and barley. Seed coat colour change from brown-red to yellow was observed in a mutant line (142-3) of B. distachyon, which was induced by chronic gamma radiation. In addition, dwarf phenotypes were observed in each of the lines 142-3, 421-2, and 1376-1. To identify causal mutations for the seed coat colour change, the three mutant lines and the wild type were subjected to whole-genome re-sequencing. After removing natural variations, 906, 1057, and 978 DNA polymorphisms were detected in 142-3, 421-2, and 1376-1, respectively. A total of 13 high-risk DNA polymorphisms were identified in mutant 142-3. Based on a comparison with DNA polymorphisms in 421-2 and 1376-1, candidate causal mutations for the seed coat colour change in 142-3 were selected. In the two independent Arabidopsis thaliana lines carrying T-DNA insertions in the AtCHI, seed colour change was observed. We propose a frameshift mutation in BdCHI1 as a causal mutation responsible for seed colour change in 142-3. The DNA polymorphism information for these mutant lines can be utilized for functional genomics in B. distachyon and cereal crops.

Developmental changes in the germinability, desiccation tolerance, hardseededness, and longevity of individual seeds of Trifolium ambiguum

BACKGROUND AND AIMS

Using two parental clones of outcrossing Trifolium ambiguum as a potential model system, we examined how during seed development the maternal parent, number of seeds per pod, seed position within the pod, and pod position within the inflorescence influenced individual seed fresh weight, dry weight, water content, germinability, desiccation tolerance, hardseededness, and subsequent longevity of individual seeds.

METHODS

Near simultaneous, manual reciprocal crosses were carried out between clonal lines for two experiments. Infructescences were harvested at intervals during seed development. Each individual seed was weighed and then used to determine dry weight or one of the physiological behaviour traits.

KEY RESULTS

Whilst population mass maturity was reached at 33-36 days after pollination (DAP), seed-to-seed variation in maximum seed dry weight, when it was achieved, and when maturation drying commenced, was considerable. Individual seeds acquired germinability between 14 and 44 DAP, desiccation tolerance between 30 and 40 DAP, and the capability to become hardseeded between 30 and 47 DAP. The time for viability to fall to 50 % (p(50)) at 60 % relative humidity and 45 degrees C increased between 36 and 56 DAP, when the seed coats of most individuals had become dark orange, but declined thereafter. Individual seed f. wt at harvest did not correlate with air-dry storage survival period. Analysing survival data for cohorts of seeds reduced the standard deviation of the normal distribution of seed deaths in time, but no sub-population showed complete uniformity of survival period.

CONCLUSIONS

Variation in individual seed behaviours within a developing population is inherent and inevitable. In this outbreeder, there is significant variation in seed longevity which appears dependent on embryo genotype with little effect of maternal genotype or architectural factors.