The Genetics and Genome-Wide Screening of Regrowth Loci, a Key Component of Perennialism in Zea diploperennis

Perenniality: From model plants to applications in agriculture

To compensate for their sessile nature, plants have evolved sophisticated mechanisms enabling them to adapt to ever-changing environments. One such prominent feature is the evolution of diverse life history strategies, particularly such that annuals reproduce once followed by seasonal death, while perennials live longer by cycling growth seasonally. This intrinsic phenology is primarily genetic and can be altered by environmental factors. Although evolutionary transitions between annual and perennial life history strategies are common, perennials account for most species in nature because they survive well under year-round stresses. This proportion, however, is reversed in agriculture. Hence, perennial crops promise to likewise protect and enhance the resilience of agricultural ecosystems in response to climate change. Despite significant endeavors that have been made to generate perennial crops, progress is slow because of barriers in studying perennials, and many developed species await further improvement. Recent findings in model species have illustrated that simply rewiring existing genetic networks can lead to lifestyle variation. This implies that engineering plant life history strategy can be achieved by manipulating only a few key genes. In this review, we summarize our current understanding of genetic basis of perenniality and discuss major questions and challenges that remain to be addressed.

Convergent evolution of the annual life history syndrome from perennial ancestors

Despite most angiosperms being perennial, once-flowering annuals have evolved multiple times independently, making life history traits among the most labile trait syndromes in flowering plants. Much research has focused on discerning the adaptive forces driving the evolution of annual species, and in pinpointing traits that distinguish them from perennials. By contrast, little is known about how 'annual traits' evolve, and whether the same traits and genes have evolved in parallel to affect independent origins of the annual syndrome. Here, we review what is known about the distribution of annuals in both phylogenetic and environmental space and assess the evidence for parallel evolution of annuality through similar physiological, developmental, and/or genetic mechanisms. We then use temperate grasses as a case study for modeling the evolution of annuality and suggest future directions for understanding annual-perennial transitions in other groups of plants. Understanding how convergent life history traits evolve can help predict species responses to climate change and allows transfer of knowledge between model and agriculturally important species.

Teosinte confers specific alleles and yield potential to maize improvement

Teosinte improves maize grain yield and broadens the maize germplasm. Seventy-one quantitative trait loci associated with 24 differential traits between maize and teosinte were identified. Maize is a major cereal crop with a narrow germplasm that has limited its production and breeding progress. Teosinte, an ancestor of maize, provides valuable genetic resources for maize breeding. To identify the favorable alien alleles in teosinte and its yield potential for maize breeding, 4 backcrossed maize-teosinte recombinant inbred line (RIL) populations were cultivated under five conditions. A North Carolina mating design II experiment was conducted on inbred lines with B73 and Mo17 pedigree backgrounds to analyze their combining ability. Abundant phenotypic variation on 26 traits of four RIL populations were found, of which barren tip length, kernel height, and test weight showed positive genetic improvement potential. The hybrid FM132 (BD138/MP116) showed a superior grain yield to that of the check, with an average yield gain of 4.86%. Moreover, inbred lines BD138 and MP048 showed a higher general grain yield combining ability than those of their corresponding checks. We screened 4,964,439 high-quality single-nucleotide polymorphisms in the BD (B73/Zea diploperennis) RIL population for bin construction and used 2322 bin markers for genetic map construction and quantitative trait loci (QTL) mapping. Via inclusive composite interval mapping, 71 QTL associated with 24 differential traits were identified. Gene annotation and transcriptional expression suggested that Zm00001eb352570 and Zm00001eb352580, both annotated as ethylene-responsive transcription factors, were key candidate genes that regulate ear height and the ratio of ear to plant height. Our results indicate that teosinte could broaden the narrow maize germplasm, improve yield potential, and provide desirable alleles for maize breeding.

Perennials as Future Grain Crops: Opportunities and Challenges

Perennial grain crops could make a valuable addition to sustainable agriculture, potentially even as an alternative to their annual counterparts. The ability of perennials to grow year after year significantly reduces the number of agricultural inputs required, in terms of both planting and weed control, while reduced tillage improves soil health and on-farm biodiversity. Presently, perennial grain crops are not grown at large scale, mainly due to their early stages of domestication and current low yields. Narrowing the yield gap between perennial and annual grain crops will depend on characterizing differences in their life cycles, resource allocation, and reproductive strategies and understanding the trade-offs between annualism, perennialism, and yield. The genetic and biochemical pathways controlling plant growth, physiology, and senescence should be analyzed in perennial crop plants. This information could then be used to facilitate tailored genetic improvement of selected perennial grain crops to improve agronomic traits and enhance yield, while maintaining the benefits associated with perennialism.

QTL Map of Early- and Late-Stage Perennial Regrowth in Zea diploperennis

Numerous climate change threats will necessitate a shift toward more sustainable agricultural practices during the 21st century. Conversion of annual crops to perennials that are capable of regrowing over multiple yearly growth cycles could help to facilitate this transition. Perennials can capture greater amounts of carbon and access more water and soil nutrients compared to annuals. In principle it should be possible to identify genes that confer perenniality from wild relatives and transfer them into existing breeding lines to create novel perennial crops. Two major loci controlling perennial regrowth in the maize relative Zea diploperennis were previously mapped to chromosome 2 (reg1) and chromosome 7 (reg2). Here we extend this work by mapping perennial regrowth in segregating populations involving Z. diploperennis and the maize inbreds P39 and Hp301 using QTL-seq and traditional QTL mapping approaches. The results confirmed the existence of a major perennial regrowth QTL on chromosome 2 (reg1). Although we did not observe the reg2 QTL in these populations, we discovered a third QTL on chromosome 8 which we named regrowth3 (reg3). The reg3 locus exerts its strongest effect late in the regrowth cycle. Neither reg1 nor reg3 overlapped with tiller number QTL scored in the same population, suggesting specific roles in the perennial phenotype. Our data, along with prior work, indicate that perennial regrowth in maize is conferred by relatively few major QTL.