Eduardo D. Munaiz

The study of genetics seeks to understand the molecular relationships that ensure the proper patterning of gene expression necessary for plant development and its responses to the environment that determine crop performance. Improvements in molecular genetics, biotechnology, and a deeper understanding of gene expression have given breeders access to major sources of phenotypic novelty in plants and allowed them to accelerate genetic gains by breeding locally adapted crops. Advances in genetics, and more recently the edition of epigenetic marks, cis-regulatory elements and gene editing have gained significant importance in crop breeding. Single-cell level studies have helped to elucidate cell heterogeneity and intercellular regulation in key tissues, enabling a more precise comprehension of the effects of plant developmental processes on phenotypes. The aim of this review is to highlight how genetic knowledge has fostered progress in crop improvement and selection. After a summary of the historical use of genetics in breeding strategies over the past 100 years, we discuss how the latest technological developments in genetics can be leveraged in complex quantitative trait improvement. Recent progress in single-cell analyses allow us to identify the subtle relationship between the genomic blueprint and cellular diversity, connecting this cellular genetic heterogeneity of a plant to specific phenotypes, that would be otherwise overlooked when using bulk cell analyses. High-throughput access to numerous epigenetic marks has also opened up new opportunities and challenges for crop genetic improvement. This progress has led to a better understanding of the role of cis-regulatory elements in determining some aspects of crop performance. Here we also discuss whether it is possible to leverage reliable variations in these regions in crop breeding, using targeted selection to manipulate traits in a wide range of crops. Finally, we outline advances in gene editing tools in crop improvement, and discuss how these could be implemented to accelerate breeding for crops adapted to new environments.

Drought‐tolerant (DT) maize ( Zea mays L.) hybrids have demonstrated better performance than non‐DT hybrids when drought events are present. The objective of this study was to assess the performance of three DT maize hybrids for whole‐plant dry matter (DM) and grain yield and forage nutritive value under conventional or Kura clover ( Trifolium ambiguum M. Bieb.) perennial groundcover (PGC) cropping systems. This study was conducted for 3 years at two locations, Arlington and Lancaster, WI. Three DT and one non‐DT maize hybrid were no‐till sown into killed Kura clover (conventional) and living Kura clover that was suppressed with herbicides (PGC). Whole‐plant maize, as for silage, was harvested at 50% kernel milk line, and grain was harvested at physiological maturity. Whole‐plant biomass was analyzed for forage nutritive value. There was no cropping system × maize hybrid interaction for any of the measured yield or nutritive value parameters. Maize hybrids in the Kura clover PGC system yielded 3.0 Mg ha ⁻¹ less whole‐plant DM and 1.5 Mg ha ⁻¹ less grain than in the conventional system, but whole‐plant forage digestibility was slightly greater with the PGC system. DT hybrids yielded slightly less than the non‐DT hybrid over both production systems. The DT hybrids demonstrated no advantage relative to a non‐DT maize hybrid in a Kura clover PCG system.

Non-Mendelian transmission of mitochondria has been well established across most eukaryotes, however the genetic mechanism that governs this uniparental inheritance remains unclear. Plants in the genus Cucumis, specifically melon and cucumber, exhibit paternal transmission of the mitochondrial (mt) DNA, making them excellent models for exploring the molecular mechanisms underlying mitochondrial transmission. Here, we develop a toolkit to screen for mutants in mitochondrial inheritance (mti), and use fine mapping to successfully identify a mitochondrially targeted endonuclease gene (MTI1) controlling mitochondrial transmission. Knockout of MTI1 results in a shift from paternal to bi-parental inheritance of the mtDNA, confirming the crucial role of MTI1 in uniparental inheritance of mitochondria. Moreover, we demonstrate that MTI1 exhibits robust endonuclease activity both in vitro and in vivo, specifically expresses in mitochondria of the fertilized ovule within 24 h of pollination. Collectively, this study reveals that a nuclear-encoded but mitochondria-targeted gene plays a causative role in governing the non-Mendelian mitochondrial inheritance, revolutionizing our knowledge about mitochondrial DNA transmission.

Increased consumption of vegetables has been recommended worldwide as a part of a healthy diet; therefore, determining gene function among breeding materials is crucial for vegetable improvement to meet the sustainable development of new vegetable varieties. However, genetic transformation is time-consuming and laborious, which limits the exploration of gene function for various vegetable crops. Virus-Induced Gene Silencing (VIGS) can perform large-scale and rapid gene silencing in plants due to a reduction in the experimental period and its independence from the stable genetic transformation, providing an excellent opportunity for functional research. VIGS can accelerate model plant research and make it easier to analyze gene function and validation in vegetable crops. Moreover, with the advent of technologies such as virus-mediated heterologous protein expression and the development of CRISPR/Cas9 technology, virus-mediated genetic tools have ushered in a new era in genetics and crop improvement. This study summarizes recent achievements in VIGS and Virus-Induced Gene Editing (VIGE) in vegetables. We also identify several challenges in the current state of VIGS technology in vegetables, serving as a guide for future research.

Senescence is an important trait in maize (Zea maisL.), a key crop that provides nutrition values and a renewable source of bioenergy worldwide. Genome-wide association studies (GWAS) can be used to identify causative genetic variants that influence the major physiological measures of senescence, which is used by plants as a defense mechanism against abiotic and biotic stresses affecting its performance. We measured four physiological and two agronomic traits that affect senescence. Six hundred seventy-two recombinant inbred lines (RILs) were evaluated in two consecutive years. Thirty-six candidate genes were identified by genome-wide association study (GWAS), and 11 of them were supported by additional evidence for involvement in senescence-related processes including proteolysis, sugar transport, and sink activity. We identified a candidate gene, Zm00001d043586, significantly associated with chlorophyll, and independently studied its transcription expression in an independent panel. Our results showed that Zm00001d043586 affects chlorophyl rate degradation, a key determinant of senescence, at late plant development stages. These results contribute to better understand the genetic relationship of the important trait senescence with physiology related parameters in maize and provide new putative molecular markers that can be used in marker assisted selection for line development.

Maize biomass from agricultural residues can be a substrate for biofuel production. However, commercial breeding programs have focused on grain yield for food and feed, and whole plant yield and nutritive value for silage, with little attention paid directly to stover yield or composition. Enhancing the energy content of crop residues with higher quality cellulosic biomass for ethanol conversion should provide a complementary use to grain use. We also question whether there is maize germplasm predisposed to dual use as second-generation biofuel. Twenty genotypes, including landraces from Spain, Atlantic, and Mediterranean Europe and genotypes derived from Iowa stiff stalk synthetic, Lancaster, and commercial hybrids were studied in a randomized complete block design across environments in Galicia (Spain) in 2010 and 2011. Germplasm was evaluated for agronomic characteristics and fiber parameters. Results show high heritability for all characteristics and parameters, ranging from 0.81 to 0.98. Principal components analysis revealed clear differences among origin of the varieties studied. Hybrids had the highest grain yield values and B73xMo17 and PR34G13 had the highest grain yield overall, at 10133 and 9349 kg/ha, respectively. European landrace varieties had lower harvest indexes (HI) than the hybrid origin, with Faro and BSL having HI of 0.43–0.47, compared to hybrid PR34613 at 0.56. Fiber concentrations were significantly correlated with yield performance, with values ranging from 0.38 to 0.61 for cob fibers and between −0.14 to −0.57 for stover fibers. Fiber concentrations were significantly different, based on the origins, in cobs but not in stover, with the Atlantic European group showing a favorable trend for cob exploitation with low acid detergent lignin and high acid detergent fiber and neutral detergent fiber values. In summary, population origin showed a reservoir of genetic diversity for breeding to improve residue quality, suggesting that adaptation played a role for stover yield and quality. European landraces could be used in prebreeding programs with stover yield and fiber quality as target traits for dual-purpose maize.

Epicuticular waxes on the surface of plant leaves are important for the tolerance to abiotic stresses and plant–parasite interactions. In the onion (Allium cepa L.), the variation for the amounts and types of epicuticular waxes is significantly associated with less feeding damage by the insect Thrips tabaci (thrips). Epicuticular wax profiles are measured using used gas chromatography mass spectrometry (GCMS), which is a labor intensive and relatively expensive approach. Biochemical spectroscopy is a non-destructive tool for measurement and analysis of physiological and chemical features of plants. This study used GCMS and full-range biochemical spectroscopy to characterize epicuticular waxes on seven onion accessions with visually glossy (low wax), semi-glossy (intermediate wax), or waxy (copious wax) foliage, as well as a segregating family from the cross of glossy and waxy onions. In agreement with previous studies, GCMS revealed that the three main waxes on the leaves of a wild type waxy onion were the ketone hentriacontanone-16 (H16) and fatty alcohols octacosanol-1 (Oct) and triacontanol-1 (Tri). The glossy cultivar “Odourless Greenleaf” had a unique phenotype with essentially no H16 and Tri and higher amounts of Oct and the fatty alcohol hexacosanol-1 (Hex). Hyperspectral reflectance profiles were measured on leaves of the onion accessions and segregating family, and partial least-squares regression (PLSR) was utilized to generate a spectral coefficient for every wavelength and prediction models for the amounts of the three major wax components. PLSR predictions were robust with independent validation coefficients of determination at 0.72, 0.70, and 0.42 for H16, Oct, and Tri, respectively. The predicted amounts of H16, Oct, and Tri are the result of an additive effect of multiple spectral features of different intensities. The variation of reflectance for H16, Oct, and Tri revealed unique spectral features at 2259 nm, 645 nm, and 730 nm, respectively. Reflectance spectroscopy successfully revealed a major quantitative trait locus (QTL) for amounts of H16, Oct, and Tri in the segregating family, agreeing with previous genetic studies. This study demonstrates that hyperspectral signatures can be used for non-destructive measurement of major waxes on onion leaves as a basis for rapid plant assessment in support of developing thrips-resistant onions.

In this review, we present a comprehensive revisit of past research and advances developed on the stay-green (SG) paradigm. The study aims to provide an application-focused review of the SG phenotypes as crop residuals for bioenergy. Little is known about the SG trait as a germplasm enhancer resource for energy storage as a system for alternative energy. Initially described as a single locus recessive trait, SG was shortly after reported as a quantitative trait governed by complex physiological and metabolic networks including chlorophyll efficiency, nitrogen contents, nutrient remobilization and source-sink balance. Together with the fact that phenotyping efforts have improved rapidly in the last decade, new approaches based on sensing technologies have had an impact in SG identification. Since SG is linked to delayed senescence, we present a review of the term senescence applied to crop residuals and bioenergy. Firstly, we discuss the idiosyncrasy of senescence. Secondly, we present biological processes that determine the fate of senescence. Thirdly, we present the genetics underlying SG for crop-trait improvement in different crops. Further, this review explores the potential uses of senescence for bioenergy crops. Finally, we discuss how high-throughput phenotyping methods assist new technologies such as genomic selection in a cost-efficient manner.

Onion ( Allium cepa ) plants with lower amounts of epicuticular waxes on foliage suffer less damage from the insect pest Thrips tabaci (onion thrips). Glossy onion accumulates significantly less epicuticular wax compared with wild-type “waxy” onion, and a single recessive locus ( gl ) has been proposed to condition this phenotype. Genetic analyses of types and amounts of epicuticular waxes were completed using two segregating families from the cross of the glossy inbreds B9885 and B9897 (both originally selected from the onion cultivar White Persian) with waxy inbred B8667 and semiglossy (intermediate amounts of waxes) inbred B5351, respectively. F ₂ progenies were grown in greenhouses and scored visually for foliar phenotypes, and amounts and types of epicuticular waxes were determined using gas chromatography-mass spectrometry (GCMS). For one F ₂ family from the cross of glossy B9885 by waxy B8667, visually scored glossy vs. waxy foliage fit a 1:3 ratio and the phenotype mapped to chromosome 8 of onion. This same region on chromosome 8 was significantly associated with amounts of the ketone hentriacontanone-16 (H16) and fatty alcohols 1-octacosanol (Oct1) and 1-triacontanol (Tri1). Visually scored F ₂ progeny from the cross of glossy B9897 × semiglossy B5351 did not fit expected models for one or two recessive loci. Significant quantitative trait loci (QTL) were revealed on chromosomes 5 and 8 controlling amounts of H16. Epistasis was detected between regions on chromosomes 1 and 8, and a 100-fold increase of H16 was conditioned by homozygous genotypes for the B5351 region on chromosome 1 and the B9885 region on chromosome 8. The three QTL model explained 41% of the phenotypic variation for amounts of H16 at logarithm of odds of 16.6. Amounts of Oct1 and Tri1 in the B9897 × B5351 family were associated with a major QTL on chromosome 1, explaining 37% to 46% of the phenotypic variation, respectively. This research demonstrates that glossy foliage of ‘White Persian’ onion is conditioned by a recessive locus on chromosome 8 for which we propose the name gl ^wp . These results are important for selection of onion with unique profiles of epicuticular waxes to reduce losses resulting from onion thrips.

Onion thrips ( Thrips tabaci ) is the main insect pest of onion ( Allium cepa ), and feeding damage routinely causes serious yield losses. Lower amounts of epicuticular waxes on onion leaves have been associated with fewer onion thrips and less feeding damage, and research is needed to assess the relationships between amounts and composition of epicuticular waxes and feeding damage by onion thrips. This study used gas chromatography mass spectroscopy to determine amounts and types of epicuticular waxes on the foliage of onion accessions that had been field-selected for lower damage from onion thrips. Hentriacontanone-16 (H16), octaconasol-1, and triacontanol-1 were the most prevalent waxes on the foliage of these selections. Amounts of H16 were significantly lower on selections visually classified as having glossy or semiglossy foliage. Semiglossy selections were identified with similar amounts of total epicuticular wax as waxy phenotypes, due primarily to lower amounts of H16 and higher amounts of other waxes. These semiglossy selections suffered significantly less feeding damage from onion thrips in a field evaluation, supporting the identification of unique wax profiles toward the development of thrips-resistant onion.