Biocultural vulnerability of traditional crops in the Indian Trans Himalaya

Traditional agricultural landscapes are vital reservoirs of biocultural heritage and agrobiodiversity, yet traditional farming systems and their unique crop landraces face increasing marginalization and genetic erosion. Using northwest Himalaya as a case study, we examine the ecological resilience and genetic diversity of an understudied traditional crop, black pea (scientific name unclear), alongside barley (Hordeum vulgare), and compare them to the introduced cash crop, green pea (Pisum sativum L.). Participatory field experiments with local farmers revealed that traditional crops outperform introduced varieties in survival and reproduction traits across sites. We generate the first whole-genome sequencing data for black peas. Clustering and nutritional analyses highlight black pea’s genetic richness and dietary potential. Our findings underscore the importance of integrating Traditional Ecological Knowledge with ecological science to sustain agrobiodiversity, enhance climate resilience, and promote sustainable food systems. We provide insights for global agri-food innovations and socio-ecological stability in fragile mountain ecosystems.

Methods
The crop dataset was collected during March-Sep 2023 during the cropping season for survival and growth performance of the three different crops. The data was collated and compared on those performance metrics. The genetic dataset was collected from paper: 

Tao Yang et al. “Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics”. Nature genetics 54.10 (2022), pp. 1553–156

This was compared with our whole genome sequencing data. We want to note that the whole genome sequencing data generated for the black pea as part of this study has been deposited on NCBI - BioSample accession SAMN44380099.

The genetic analysis consists of the following files. The files are the covariance matrices for each of the 7 chromosomes for black peas. They can be read in R using the read.table() function with the header as False since the file is a matrix with 18 rows and 18 columns. 

    Pea_n18_NC_066579.covar
    Pea_n18_NC_066580.covar
    Pea_n18_NC_066581.covar
    Pea_n18_NC_066582.covar
    Pea_n18_NC_066583.covar
    Pea_n18_NC_066584.covar
    Pea_n18_NC_066585.covar

In addition, the file peapca_supplement_genome.csv provides SRR and accension details for the Pisum species and subspecies used to compare our black pea sample with. The data was collected from Tao Yang 2022 paper.

The ecological analysis can be performed using 2023_crop_data. The csv file is read in R using read.csv function. The columns correspond to flowering (proportion of flowering plants), survival (proportion of seeds germinating), leaf (length in cm), stem height (length in cm), number of pods after x days, where x is added to the column names. The rows correspond to the values for the type of crop (green pea, black pea, barley), according to site (Kibber, Kiamo, Tashigang, and Thinam) as well as the replicates.