Editorial: Genome-Wide Identification of Functional Markers to Enhance Molecular Breeding Efforts in Agriculturally Important, Underutilized, and Less Explored Plant Species

Rajni Parmar^1*Sapna Thakur²Ram Kumar Sharma²

• ¹Tennessee State University, Nashville, United States
• ²Institute of Himalayan Bioresource Technology, CSIR, Palampur, India

Agriculture is the primary energy source for humans; however, it is facing two major challenges at present -the growing population and rapid climate change causing extreme weather events, which are expected to persist in the future as well. By the end of this century, the global population is expected to grow and reach 10-12 billion, highlights the importance of increasing total food production to feed the rapidly growing population. Therefore, it becomes very important to accelerate agricultural research with a goal to acquire deeper understanding of essential traits for future breeding targets. The advances in genomic technologies in the last two decades have contributed immensely to agricultural research. This issue presents a collection of four original research articles, that have utilized genome-wide identification of potential genes and association studies to investigate and address several challenging biological questions.In the current issue, a study done by Liu et al., 2003 was reported wherein genome-wide association analysis was performed in an economically important crop (rice), targeting traits like panicle length (PL), total grain number per panicle (TGP), filled grain number per panicle (FGP), seed setting rate (SSR) and grain weight per panicle (GWP). Elucidation of underlying genetic players involved in these traits is important for molecular breeding in rice to improve yield. Panicle traits are quantitative in nature and is substantially affected by environment: therefore, these traits require more comprehensive and extensive research to precisely determine their corresponding QTLs (Quantitative Trait Loci) and underlying genes responsible for phenotypic heterogeneity. The authors performed GWAS on data collected over three years and were able to identify four QTLs for PL, three QTLs for FGP and one QTL for TGP, GWP, SSR. These QTLs were detected in both GLM (General Linear Model) and MLM (Mixed Linear Model) analysis and BLUP (Best Linear Unbiased Prediction) was used to improve the accuracy of GWAS via modelling complex interaction between environment and genotypes. Furthermore, two candidate genes viz., LOC_Os01g43700 (Cytochrome P450 protein), and LOC_Os09g25784 (Auxin-induced protein, 5NG4) were also identified that were closely associated with PL; and another, LOC_Os04g47890 (MYB family transcription factor), with FGP, GWP and TGP. In this study, along with mining of excellent alleles related to panicle traits in rice, ten parental lines with favorable alleles associated with yield traits was also recommended for future molecular breeding.Two additional noteworthy studies (Shen et al., 2024 andLi et al.,2024) reported in the current issue were in wild potato (Solanum pinnatisectum) and common potato (Solanum tuberosum L.). Undertaking studies in both wild and cultivated species helps to better understand genetic diversity and to identify beneficial traits which can help in enhancing adaptability and resilience of the crop.This issue includes a study reporting the first draft chromosome-level genome assembly of Solanum pinnatisectum, which has strong resistance against Phytophthora infestans and creates genomic resources fundamental for understanding disease resistance mechanisms. A high-quality genome assembly of 664Mb size with 34,245 genes was reported and a total of 303 NBS-coding disease resistance genes were also identified. Additionally, it was found that S. pinnatisectum harbors a high number of unique genes and its comparative genomic analysis with cultivated species reveals that pathways related to plant-pathogen interaction and phagosomes were highly enriched in wild species, suggest their putative role in plant resistance. An additional 68 genes involved in resistance to late blight in potato were also reported on the basis of RNA seq analysis. This study reported a high quality-reference genome assembly using Oxford Nanopore long read sequencing and Hi-C technologies, which has resulted in creation of a valuable genomic resource of disease resistance genes which can be incorporated in modern breeding programs.Another important investigation on cultivated potato (Solanum tuberosum L.) in this issue (citation?) has presented the genome-wide identification and structural characterization of the FBA (Fructose-1, 6-bisphosphate aldolase) gene family (Li et al.,2024). This gene is involved in photosynthesis and energy metabolism and comprehensive genomic insight into StFBA gene, can be utilized to improve the efficiency of photosynthesis, tuber development and abiotic stress response. Two classes (Eight Class I and one class II) of StFBA genes were reported on the basis of their structure, function and phylogenetic relationship. The evolutionary relationship of the FBA gene family with six other species including Arabidopsis, rice, tomato, eggplant, tobacco and wheat was reported, finding FBA genes of potato and tomato to be closely related. Furthermore, colinearity analyses between potato, tomato and Arabidopsis revealed that segmental duplication is responsible for the expansion of the potato FBA gene family. After performing promoter and expression analysis, the authors concluded that StFBA genes have cis-regulatory elements coupled with light and stress response; and blue light increases StFBA3, StFBA8 and StFBA9 expression in stolon, leaf and tuber. Collectively, the outcome of this study suggests that these genes can be utilized to improve photosynthesis, induction and expansion of tubers, and abiotic stress response.The last and pivotal study published by Kim et al.,2023 in this issue was on Northern red oak (Quercus rubra), which is an economically and ecologically important tree in North America and Southeastern Canada. The strong and durable hardwood of this tree is used as floorboard and building materials and Q. rubra is a key species for woody plant research, as it is one of the most important red oak lumber species. The genome-wide identification and expression analysis of the PKF (Phosphofructokinase) gene which plays a key role in the glycolytic pathway was carried out. A total of 14 QrPFK genes were identified, and phylogenetic analysis divided them into two groups: eleven attributed to PFK and three to PFP (pyrophosphate-fructose-6-phosphate phosphotransferase). Furthermore, the expression analysis revealed that all 14 QrPFK genes have similar expression in leaves, however, stem and roots exhibit differential expression of these genes. This study has uncovered a critical role of PFK gene function in Q. rubra, laying a foundation for future investigations.