We used conserved domains in the major class (nucleotide binding site plus leucine-rich repeat) of dicot resistance (R) genes to isolate related gene fragments via PCR from the monocot species rice and barley. Peptide sequence comparison of dicot R genes and monocot R-like genes revealed shared motifs but provided no evidence for a monocot-specific signature. Mapping of these genes in rice and barley showed linkage to genetically characterized R genes and revealed the existence of mixed clusters, each harboring at least two highly dissimilar R-like genes. Diversity was detected intraspecifically with wide variation in copy number between varieties of a particular species. Interspecific analyses of R-like genes frequently revealed nonsyntenic map locations between the cereal species rice, barley, and foxtail millet although tight collinear gene order is a hallmark of monocot genomes. Our data suggest a dramatic rearrangement of R gene loci between related species and implies a different mechanism for nucleotide binding site plus leucine-rich repeat gene evolution compared with the rest of the monocot genome.

https://www.pnas.org/content/pnas/95/1/370.full.pdf

Rapid reorganization of resistance gene homologues in cereal genomes

The use of polymorphic single genes to facilitate the process of plant breeding was proposed early in this Century (Sax, 1923). The basic principle is that selection for characters with easily detectable phenotypes can simplify the recovery of genes of interest linked to them and more difficult to score. The first marker loci available were those that have an obvious impact on the morphology of the plant. Genes that affect form, coloration, male sterility or disease resistance among others have been genetically analysed in many plant species. In some well characterized crops like maize, tomato, pea, barley or wheat, tens or even hundreds of such genes have been assigned to different chromosomes (O’Brien, 1990).

Marker-assisted selection

indicated that genetic improvement usually accounted for about one-half of the total yield increase, with the This paper was presented as part of the symposium entitled “Postremainder attributed to changes in cultural practices Green Revolution Trends in Crop Yield Potential: Increasing, Stagnant or Greater Resistance to Stress.” In this presentation, we have such as increased rates of mineral fertilizers and the use focused on (i) uses of marker technology in determining the genetic of herbicides for weed control and pesticides for control basis of phenotypic expression and the manipulation of phenotypic of insects and diseases. Duvick (1997) suggested that the variation in plants. This included the use of markers in understanding increased grain yielding ability of these widely successful heterosis, in attempts to improve hybrid predictions, in quantitative hybrids was due primarily to improved tolerance of abitrait locus (QTL) identification and mapping, in marker-assisted selecotic and biotic stresses, coupled with the maintenance tion (MAS), and in enhancing breeding success in the development of the ability to maximize yield per plant under nonof improved lines and hybrids; (ii) the role of genomics in developing stress growing conditions. a precise understanding of the genetic basis of phenotypic expression Opportunities for gains resulting from changes in culwhich will then provide more precision in the manipulation of phenotural practices are limited (particularly in the USA and typic variation; and (iii) some attempts to integrate marker technology and genomics into empirical breeding strategies. In addition, we have other developed countries). Therefore, future gains in focused on what has been successful as well as what has fallen short the productivity of most crops may depend almost enof expectations, and have suggested some of the possible reasons for tirely on genetic improvements. In fact, environmental the lack of success. Because of page limitations, we could not include concerns may cause a reduction in the use of agricultural an exhaustive review of the plant literature and have limited many chemicals and fertilizers. Also, many parts of the world of our examples to investigations in maize (Zea mays L). may have limited supplies of such chemicals and plant nutrients. Therefore, plant breeders will need to develop and apply new technology (such as marker-assisted seT global ability to provide adequate amounts of lection) at a faster pace to more effectively improve the food, feed, and fiber from domesticated crop plants yield potentials of crop plants for the ever increasing has resulted largely from the collective empirical breedglobal human population as well as for the changes in ing efforts of farmers and plant breeders spanning many consumer preferences. millennia. The continued increases in plant productivity have resulted from artificial selection, either conscious Quantitative Traits and QTLs or unconscious, on the phenotypic expressions of the A majority of economically important plant traits, targeted species. Prior to the 20th century, plant breedsuch as grain or forage yield, can be classified as ing was largely an art with little or no knowledge of multigenic or quantitative. Even traits considered to be genetic principles. Although plant improvement since more simply inherited, such as disease resistance, may the rediscovery of Mendel’s principles has involved both be “semi-quantitative” for which trait expression is govart and science, the contributions of science will unerned by several genes (e.g., a major gene plus several doubtedly assume a much greater role as new technolmodifiers). The challenge to use strategically new techogy becomes more widely used and as additional gains nology (such as DNA-based markers) to increase the in agricultural productivity are required to support a contribution of “science” to the “art plus science” equagreater global population. New opportunities to use getion for plant improvement therefore applies to most, if notypic selection, or combinations of genotypic and phenot all, traits of importance in plant breeding programs. notypic selection, to increase yield potentials are emergAlthough the focus of this symposium is on yield potening at an ever-increasing pace. tial, that yield must be harvestable. Therefore, traits On the basis of a comparison of 36 widely grown such as standability (or lodging resistance), disease resishybrids adapted to central Iowa and released at intervals tance, and insect resistance must also be considered. from 1934 to 1991, Duvick (1997) reported that the Historically, early researchers in quantitative genetics increase in maize grain yield during that time span averquestioned whether the inheritance of these continuaged nearly 74 kg ha21 yr21. Hybrid comparisons were ously distributed traits was Mendelian (Comstock, based on side-by-side trials, so all of the gain could 1978). The answer to this question has major implicabe attributed to genetic improvement. Earlier studies tions in the consideration of the use of markers for plant breeding programs. During the past century, both plant C. Stuber, USDA-ARS and Dep. of Genetics, N.C. State Univ., Raleigh, NC 27695-7614; M. Polacco, USDA-ARS, Plant Genetics Res. and animal geneticists have obtained convincing eviUnit, Univ. of Missouri, Columbia, MO 65211; M. Senior, Novartis dence that Mendelian principles apply to quantitative Agribusiness Biotechnology Research, Inc., 3054 Cornwallis Rd., Research Triangle Park, NC 27709. Received 28 Dec. 1998. *CorrespondAbbreviations: BAC, bacterial artificial chromosome; MAS, markering author (cstuber@ncsu.edu). assisted selection; QTL, quantitative trait locus, RFLP, restriction fragment length polymorphism; YAC yeast artificial chromosome. Published in Crop Sci. 39:1571–1583 (1999).

Synergy of Empirical Breeding, Marker-Assisted Selection, and Genomics to Increase Crop Yield Potential

Barley (Hordeum vulgare ssp. vulgare) is an excellent model for understanding agricultural responses to climate change. Its initial domestication over 10 millennia ago and subsequent wide migration provide striking evidence of adaptation to different environments, agro-ecologies and uses. A bottleneck in the selection of modern varieties has resulted in a reduction in total genetic diversity and a loss of specific alleles relevant to climate-smart agriculture. However, extensive and well-curated collections of landraces, wild barley accessions (H. vulgare ssp. spontaneum) and other Hordeum species exist and are important new allele sources. A wide range of genomic and analytical tools have entered the public domain for exploring and capturing this variation, and specialized populations, mutant stocks and transgenics facilitate the connection between genetic diversity and heritable phenotypes. These lay the biological, technological and informational foundations for developing climate-resilient crops tailored to specific environments that are supported by extensive environmental and geographical databases, new methods for climate modelling and trait/environment association analyses, and decentralized participatory improvement methods. Case studies of important climate-related traits and their constituent genes - including examples that are indicative of the complexities involved in designing appropriate responses - are presented, and key developments for the future highlighted.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.13266

Barley: a translational model for adaptation to climate change

Total and soluble beta-glucan content and effects of various treatments of barley grain on extractability and molecular characteristics of soluble beta-glucan were studied. Four types of hulless barley (normal, high amylose, waxy, and zero amylose waxy) from 29 registered and experimental genotypes were analyzed. For each, moisture, protein, amylose, 100 kernel weight, starch, beta-glucan (total and soluble), beta-glucanase activity, and slurry viscosity were determined. Significant differences in total beta-glucan were observed among the groups, with average values of 7. 49%, 6.86%, 6.30%, and 4.38% for high amylose, waxy, zero amylose waxy, and normal barley, respectively. The extractability of beta-glucan in high amylose barley was relatively low (20.6-29.7%) compared to that in normal (29.8-44.3%), zero amylose waxy (34.0-52. 5%), and waxy (36.7-52.7%) barley genotypes. Viscosity of barley flour slurries was affected by the content of soluble beta-glucans, beta-glucanase activity, and molecular weight of beta-glucans. Hydrothermal treatments (autoclaving and steaming) of barley had no effect on extractability of beta-glucans, but prevented enzymic hydrolysis of beta-glucans, and thereby substantially improved their molecular weight. The addition of enzymes (protease and esterase) during extraction and/or physical treatments (sonication) increased extractability of beta-glucans from barley.

Variation in total and soluble β-glucan content in hulless Barley : Effects of thermal, physical, and enzymic treatments

Eighty-three third backcross lines which comprise a set of near isogenic lines (NIL's) of the barley cultivar ‘Clipper’ but each carrying a different chromosomal segment from Hordeum spontaneum, marked with a distinct isozyme, were tested for resistance to three races of the barley leaf rust pathogen (Puccmia hordei). Fourteen lines showed resistance to at least one race and three showed resistance to all three races. The resistance in two of these lines was controlled by separate, single partially dominant genes. In one case the resistance gene named Rph1O was on chromosome 3 and linked (r = 0.15 ±0.05) with the isozyme locus Est2. In the second case, the gene (Rph11) was on barley chromosome 6 and linked (r = 0.07±0.02) with the isozyme locus Acp3 and (r = 0.11±0.02) with Dip2.

Linkage of Rust Resistance Genes from Wild Barley (Hordeum spontaneum) with Isozyme Markers

The scald susceptible barley cultivar 'Clipper' and a third-backcross (BC 3 ) line homozygous for the Rrs14 scald resistance gene that originally came from Hordeum vulgare ssp. spontaneum were grown in replicated field trials. The level of resistance that Rrsl4 confers against field populations of the pathogen Rhynchosporium secalis, the causal agent of scald disease, was evaluated. The Rrs14 BC 3 line exhibited 80% and 88% less leaf damage than Clipper' in 1995 and 1996, respectively. Given this effectiveness of Rrs14, research was undertaken to identify a linked marker locus suitable for indirect selection of Rrs14. Based on linkage to a set of previously mapped loci, Rrs14 was positioned to barley chromosome 1H between the seed storage protein (hordein) loci Hor1 and Hor2, approximately 1.8 cM from the latter locus. The Hor2 locus is thus an ideal codominant molecular marker for Rrs14. The tight linkage between Rrsl4 and Hor2 and the availability of alternative biochemical and molecular techniques for scoring Hor2 genotypes, permits simple indirect selection of Rrsl4 in barley scald resistance breeding programmes.

Genetic mapping of the barley Rrs14 scald resistance gene with RFLP, isozyme and seed storage protein markers

Fifty-six accessions of Hordeum spontaneum from various Israeli habitats were hybridized with, and their progeny backcrossed three times to H. vulgare cv. ‘Clipper’. Selected chromosome segments marked by one of 24 isozyme loci were transferred to form 84 backcross lines which were nearly isogenic with ‘Clipper’. Each line was made homozygous for a single isozyme-marked segment. These lines were evaluated in preliminary and advanced field trials. The yield, malt extract percentage and grain size of the lines approached or equalled, and sometimes significantly surpassed, that of ‘Clipper’ and more recent commercial cultivars. Three isozyme-marked segments were combined in pairs and the three resultant doubly-marked lines were compared with the reconstituted parental, singly-marked lines and with the ‘Clipper’ recombinant from the same F2-array. The additive effects of single segments on yield or gram size were not significant, whereas half of the six interactions were significant, but in the unfavorable direction. It was concluded that near-isogenic lines can identify segments of wild barley germplasm that are useful for improving yield, but that pairs of these from different habitats may interact unfavourably.

Use of Isozyme‐Marked Segments from Wild Barley (Hordeum spontaneum) in Barley Breeding

The carbohydrate content of Hordeum spotaneum lines collected from 23 diverse environments in Israel was investigated. The range in composition was sucrose: 0.83—1.15%; trisaccharides): 0.48—1.16% total free and combined fructose: 1.2—4.2%; pentosans: 4.2—9.9%; and fl3), (14)-β-glucans: 4.5—13.2%. The high pentosan and β-glucan content in some lines would cause quality problems if found in malting barleys.

Variation in the Carbohydrate Composition of Wild Barley (Hordeum spontaneum) Grain

Isoelectric focusing (IEF) and immunoblotting were used to detect genetic variants of malt endopeptidase (MEP1), an enzyme related to malting quality in barley and coded by the CepB locus on barley chromosome 3 (= 3H). A variant was found in a Turkish accession of wild barley (Hordeum vulgare ssp. spontaneum). The self progeny of a hybrid between this accession and the barley cultivar ‘Clipper’ were analyzed for recombination between the CepB locus and other isozyme loci. The estimates of recombination linked the CepB locus to an NADH diaphorase locus (Ndh2), which in turn was linked to the seedling esterase complex (Est1, Est2, and Est4) situated near the distal end of the long arm of chromosome 3. The Ndh2 locus was independent of two other NADH dehydrogenase loci (Ndh3, Ndh5) which were mapped on barley chromosome 5 (= 1H) in relation to the three hordein loci (Hor1, Hor2, and Hor3).

A. H. D. Brown

Papers

Linkage of Rust Resistance Genes from Wild Barley (Hordeum spontaneum) with Isozyme Markers

Genetic mapping of the barley Rrs14 scald resistance gene with RFLP, isozyme and seed storage protein markers

Use of Isozyme‐Marked Segments from Wild Barley (Hordeum spontaneum) in Barley Breeding

Variation in the Carbohydrate Composition of Wild Barley (Hordeum spontaneum) Grain

Mapping of Malt Endopeptidase, NADH Diaphorase and Esterase Loci on Barley Chromosome 3L