bims-plasge 2025-04-27 papers

Mol Biol Rep. 2025 Apr 21. 52(1): 406

Genomics assisted mapping of earliness in pea (Pisum sativum L.).

Parteek Kumar, Saurabh Yadav, Manisha Rani, Deepika Narang, Deepak Singla, Rajinder Kumar Dhall, Parveen Chhuneja, Priti Sharma.

BACKGROUND: Garden pea (Pisum sativum L.), is a temperate crop belonging to the Leguminosae family. Early maturing pea varieties complete their growth cycle in ∼80-90 days and fits very well within the crop rotation of rice, wheat, and maize, thereby providing an extra source of income to the farmers. Identification of genes associated with the earliness is very important for developing early maturing pea varieties.
METHODS AND RESULTS: In the present study we investigated the genetics of earliness and identified the putative genomic regions associated with the earliness in F2 population derived from a cross between early-maturing (Matar Ageta-10) and late-maturing (Punjab-89) pea varieties using BSA-Seq approach. Genetic analysis revealed that earliness follows a monogenic recessive inheritance pattern. Two extreme phenotypic pools were constructed by identifying ten extreme early and ten extreme late plants from the F2 population, and QTL-seq analysis was performed to obtain major genomic region of 6.5 Mb located at 418.46 Mb to 424.97 Mb on chromosome 7 and has been designated as PsE7. Further, a total of 907 SNPs were identified within this 6.5 Mb genomic region of which seven SNPs were validated through KASP markers. Among these, one marker namely PS423028253 showed association with the earliness trait at distance of 1.7 cM.
CONCLUSION: This novel genomic region along with KASP marker (PS423028253) identified in this study could be used for marker-assisted selection in pea breeding programs and will aid in the identification of the candidate genes in future studies.

Keywords: BSA-seq; Earliness; Inheritance; KASP; Marker-assisted selection; SNPs

DOI: https://doi.org/10.1007/s11033-025-10506-2

Nature. 2025 Apr 23.

Genomic and genetic insights into Mendel's pea genes.

Mendel1 studied in detail seven pairs of contrasting traits in pea (Pisum sativum), establishing the foundational principles of genetic inheritance. Here we investigate the genetic architecture that underlies these traits and uncover previously undescribed alleles for the four characterized Mendelian genes2-7, including a rare revertant of Mendel's white-flowered a allele. Primarily, we focus on the three remaining uncharacterized traits and find that (1) an approximately 100-kb genomic deletion upstream of the Chlorophyll synthase (ChlG) gene disrupts chlorophyll biosynthesis through the generation of intergenic transcriptional fusion products, conferring the yellow pod phenotype of gp mutants; (2) a MYB gene with an upstream Ogre element insertion and a CLE peptide-encoding gene with an in-frame premature stop codon explain the v and p alleles, which disrupt secondary cell wall thickening and lignification, resulting in the parchmentless, edible-pod phenotype; and (3) a 5-bp exonic deletion in a CIK-like co-receptor kinase gene, in combination with a genetic modifier locus, is associated with the fasciated stem (fa) phenotype. Furthermore, we characterize genes and alleles associated with diverse agronomic traits, such as axil ring anthocyanin pigmentation, seed size and the 'semi-leafless' form. This study establishes a foundation for fundamental research, education in biology and genetics, and pea breeding practices.

DOI: https://doi.org/10.1038/s41586-025-08891-6

Physiol Plant. 2025 Mar-Apr;177(2):177(2): e70231

Highly variable mitochondrial chromosome content in a holoparasitic plant due to recurrent gains of foreign circular DNA.

Leonardo Martin Gatica-Soria, M Emilia Roulet, Walter D Tulle, Hector A Sato, M Eugenia Barrandeguy, M Virginia Sanchez-Puerta.

Multichromosomal mitochondrial genomes (mtDNAs) in eukaryotes exhibit remarkable structural diversity, yet intraspecific variability and the origin of the individual chromosomes remain poorly understood. We focus on a holoparasitic angiosperm with an mtDNA consisting of 65 chromosomes largely composed of foreign DNA acquired by horizontal gene transfer (HGT) from its mimosoid hosts. The frequency, timing and population dynamics of these HGT events have not been examined. Here, we sampled different individuals of the holoparasite Lophophytum mirabile, along with their host plants, to assess mtDNA intraspecific variability and capture recent events that may bring insights into the HGT process. We also gathered mitochondrial data from 43 mimosoids to identify older and recent HGT events and assess precisely the proportion of foreign DNA. Through comparative genomic and evolutionary analyses, we uncovered great intraspecific variability in chromosome content and defined the mitochondrial pangenome of L. mirabile with 105 distinct chromosomes. The estimated foreign content reaches 93.5% of the mtDNA, including 73 fully foreign chromosomes that support the circle-mediated HGT model as a key mechanism for their acquisition. We inferred recurrent DNA transfers from the host plants, leading to new mitochondrial chromosomes that replicate autonomously. Our results emphasize the importance of adopting a pangenomic approach to fully capture the genetic diversity and evolution of multichromosomal mitochondrial genomes. This study shows that HGT can strongly influence the mtDNA content and generate enormous intraspecific variability even in geographically close individuals.

DOI: https://doi.org/10.1111/ppl.70231