Genome, Transcriptome, and Germplasm Sequencing Uncovers Functional Variation in the Warm-Season Grain Legume Horsegram Macrotyloma uniflorum (Lam.) Verdc.

Abstract

Horsegram is a grain legume with excellent nutritional and remedial properties and good climate resilience, able to adapt to harsh environmental conditions. Here, we used a combination of short- and long-read sequencing technologies to generate a genome sequence of 279.12Mb, covering 83.53% of the estimated total size of the horsegram genome, and we annotated 24,521 genes. De novo prediction of DNA repeats showed that approximately 25.04% of the horsegram genome was made up of repetitive sequences, the lowest among the legume genomes sequenced so far. The major transcription factors identified in the horsegram genome were bHLH, ERF, C2H2, WRKY, NAC, MYB, and bZIP, suggesting that horsegram is resistant to drought. Interestingly, the genome is abundant in Bowman–Birk protease inhibitors (BBIs), which can be used as a functional food ingredient. The results of maximum likelihood phylogenetic and estimated synonymous substitution analyses suggested that horsegram is closely related to the common bean and diverged approximately 10.17 million years ago. The double-digested restriction associated DNA (ddRAD) sequencing of 40 germplasms allowed us to identify 3,942 high-quality SNPs in the horsegram genome. A genome-wide association study with powdery mildew identified 10 significant associations similar to the MLO and RPW8.2 genes. The reference genome and other genomic information presented in this study will be of great value to horsegram breeding programs. In addition, keeping the increasing demand for food with nutraceutical values in view, these genomic data provide opportunities to explore the possibility of horsegram for use as a source of food and nutraceuticals.

Mapping of genomic regions associated with dwarfing and the determinate growth habit in horsegram (Macrotyloma uniflorum)

“…The plant height and determinate growth habit are the most important traits required for the modification of the plant architecture of a crop plant making it suitable for mechanical harvesting in commercial cultivation. Various breeding techniques, such as conventional (Chahota et al 2005), mutation (Chahota et al 2013) and molecular (Chahota et al 2020;Mahesh et al 2021), are being adopted by the breeders for the successful implication of useful traits in horsegram. SSRs are present on both the coding as well as non-coding regions (Chung et al 2006;Rajendrakumar et al 2007) having a low degree of repetition per locus (5-100) with a high degree of length polymorphism (Tautz 1993;Zane et al 2002;Parida et al 2009), thus, they are the markers of choice that are used in the present study.…”

Genome-Wide Association Studies for Identification of Novel QTLs Related to Agronomic Traits in Horsegram (Macrotyloma uniflorum)

“…The United States National Academy of Sciences has recognized this crop as an important food source for future (Tropical Legumes: Resources for the Future, 1979). Unfortunately, in horsegram limited scientific knowledge has been created in comparison to other pulses like Vigna radiate and Cajanus cajan, however, in the last decade with the advent in the next generation sequencing technology, few efforts have been made to understand important traits in horsegram of agronomic importance (Bhardwaj, et al, 2013;Kaldate, et al, 2017;Mahesh, et al, 2021;Tanin, et al, 2022; Tropical Legumes: Resources for the Future, 1979).…”

Genome-wide association studies for identification of novel QTLs related to four agronomic traits in Horsegram (Macrotyloma uniflorum)

“…The United States National Academy of Sciences has recognized this crop as an important food source for future (Tropical Legumes: Resources for the Future, 1979). Unfortunately, in horsegram limited scienti c knowledge has been created in comparison to other pulses like Vigna radiate and Cajanus cajan, however, in the last decade with the advent in the next generation sequencing technology, few efforts have been made to understand important traits in horsegram of agronomic importance (Bhardwaj, et al, 2013;Kaldate, et al, 2017;Mahesh, et al, 2021;Tanin, et al, 2022; Tropical Legumes: Resources for the Future, 1979).…”