About 12,000 years ago, humans began the transition from hunter-gathering to a sedentary, agriculture-based society. From its origins in the Near East, farming expanded throughout Europe, Asia and Africa, together with various domesticated plants and animals. Where, how and why agriculture originated is still debated. But newer findings, on the basis of genome-wide measures of genetic similarity, have traced the origins of some domesticated cereals to wild populations of naturally occurring grasses that persist in the Near East. A better understanding of the genetic differences between wild grasses and domesticated crops adds important facets to the continuing debate on the origin of Western agriculture and the societies to which it gave rise.

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Genetics and geography of wild cereal domestication in the near east

In recent years, considerable emphasis has been placed on the development of molecular markers to be used for a variety of objectives. This review attempts to give an account of different molecular markers—restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), sequence-tagged sites (STS), DNA amplification fingerprinting (DAF), amplified fragment length polymorphisms (AFLPs) and microsatellites (STMS)—currently available for genome mapping and for tagging different traits in wheat. Other markers, including microsatellite-primed polymerase chain reaction (MP-PCR), expressed sequence tags (ESTs) and single nucleotide polymorphisms (SNPs) are also discussed. Recent information on synteny in cereal genomes, marker-assisted selection, marker validation and their relevance to cereal breeding in general and wheat breeding in particular are also examined.

Molecular markers and their applications in wheat breeding.

A set of 114 recombinant inbred lines of the 'International Triticeae Mapping Initiative' mapping population was grown during the seasons 1997, 1998, 1999 and 2000 under several environments. Twenty morphological (glume colour, awn colour, waxiness, leaf erectness, peduncle length), agronomical (ear emergence time, flowering time, grain filling time, ear length, plant height, lodging, grain number, thousand-grain-weight, grain weight per ear, grain protein content, winter hardiness) and disease resistance (powdery mildew, yellow rust, leaf rust, fusarium) traits were studied. Not all traits were scored in each experiment. In total 210 QTLs with a LOD threshold of >2.0 (minor QTLs) were detected of which 64 reached a LOD score of >3.0 (major QTLs). Often QTLs were detected in comparable positions in different experiments. Homologous and homoeologous relationships of the detected QTLs, and already described major genes or QTLs determining the same traits in wheat or other Triticeae members, are discussed.

Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat ( Triticum aestivum L.).

A population of 96 doubled haploid lines (DHLs) was prepared from F1 plants of the hexaploid wheat cross Chinese Spring × SQ1 (a high abscisic acid-expressing breeding line) and was mapped with 567 RFLP, AFLP, SSR, morphological and biochemical markers covering all 21 chromosomes, with a total map length of 3,522 cM. Although the map lengths for each genome were very similar, the D genome had only half the markers of the other two genomes. The map was used to identify quantitative trait loci (QTLs) for yield and yield components from a combination of 24 site × treatment × year combinations, including nutrient stress, drought stress and salt stress treatments. Although yield QTLs were widely distributed around the genome, 17 clusters of yield QTLs from five or more trials were identified: two on group 1 chromosomes, one each on group 2 and group 3, five on group 4, four on group 5, one on group 6 and three on group 7. The strongest yield QTL effects were on chromosomes 7AL and 7BL, due mainly to variation in grain numbers per ear. Three of the yield QTL clusters were largely site-specific, while four clusters were largely associated with one or other of the stress treatments. Three of the yield QTL clusters were coincident with the dwarfing gene Rht-B1 on 4BS and with the vernalisation genes Vrn-A1 on 5AL and Vrn-D1 on 5DL. Yields of each DHL were calculated for trial mean yields of 6 g plant−1 and 2 g plant−1 (equivalent to about 8 t ha−1 and 2.5 t ha−1, respectively), representing optimum and moderately stressed conditions. Analyses of these yield estimates using interval mapping confirmed the group-7 effects on yield and, at 2 g plant−1, identified two additional major yield QTLs on chromosomes 1D and 5A. Many of the yield QTL clusters corresponded with QTLs already reported in wheat and, on the basis of comparative genetics, also in rice. The implications of these results for improving wheat yield stability are discussed.

A high-density genetic map of hexaploid wheat (Triticum aestivum L.) from the cross Chinese Spring × SQ1 and its use to compare QTLs for grain yield across a range of environments

This chapter describes a procedure for Agrobacterium-mediated wheat transformation. Freshly isolated immature embryos, precultured immature embryos, or embryogenic calli are inoculated with a disarmed A. tumefaciens strain C58 (ABI) harboring the binary vector pMON18365 containing the beta-glucuronidase (GUS) gene with an intron, and a selectable marker, neomycinphosphotranferase (NPT) II gene. The inoculated explants are selected on callus induction medium with the selective agent G418 for approximately 2 wk. The resistant callus pieces that develop are then transferred onto medium with the selective agent and reduced plant growth regulators for plant regeneration and further selection. It takes approximately 2.5 to 3 mo from inoculation to the establishment of R0 plants in soil. All the transformants should be morphologically normal and set seeds. Approximately 35% of the transgenic plants have a single copy of the transgene based on data obtained from previous experiments.

Wheat ( Triticum aestivum L.)

A genetic linkage map of tetraploid wheat [Triticum turgidum (L.) Thell.] was constructed using segregation data from a population of 65 recombinant inbred lines (RILs) derived from a cross between the durum wheat cultivar Messapia and accession MG4343 of T. turgidum (L.) Thell. ssp dicoccoides (Korn.) Thell. A total of 259 loci were analysed, including 244 restriction fragment length polymorphisms (RFLPs), one PCR (polymerase chain reaction) marker (a sequence coding for a LMW (low-molecular-weight) glutenin subunit gene located at the Glu-B3 locus), seven biochemical (six seed-storage protein loci and one isozyme locus) and seven morphological markers. A total of 213 loci were mapped at a LOD≥3 on all 14 chromosomes of the A and B genomes. The total length of the map is 1352 cM and the average distance between adjacent markers is 6.3 cM. Forty six loci could not be mapped at a LOD≥3. A fraction (18.6%) of the markers deviated significantly from the expected Mendelian ratios; clusters of loci showing distorted segregation were found on chromosomes 1B, 3AL, 4AL, 6AL and 7AL. The durum wheat map was compared with the published maps of bread wheat using several common RFLP markers and general features are discussed. The markers detected the known structural rearrangements involving chromosomes 4A, 5A and 7B as well as the translocation between 2B-6B, but not the deletion on 2BS. This map provides a useful tool for analysing and breeding economically important quantitative traits and for marker-assisted selection, as well as for studies of genome organisation in small grain cereal species.

A genetic linkage map of durum wheat

Grain protein content (GPC) in durum wheat (Triticum turgidum var. durum) is negatively correlated with grain yield. To evaluate possible genetic interrelationships between GPC and grain yield per spike, thousand-kernel weight and kernel number per spike, quantitative trait loci (QTL) for GPC were mapped using GPC-adjusted data in a covariance analysis on yield components. Phenotypic data were evaluated in a segregating population of 120 recombinant inbred lines derived from crossing the elite cultivars Svevo and Ciccio. The material was tested at five environments in southern Italy. QTL were determined by composite interval mapping based on the Svevo × Ciccio linkage map described in Gadaleta et al. (2009) and integrated with DArT markers. The close relationship between GPC and yield components was reflected in the negative correlation between the traits and in the reduction of variance when GPC values were adjusted to yield components. Ten independent genomic regions involved in the expression of GPC were detected, six of which were associated with QTL for one or more grain yield components. QTL alleles with increased GPC effects were associated with QTL alleles with decreased effects on one or more yield component traits, or vice versa (i.e. the allelic effects were in opposite direction). Four QTL for GPC showed always significant effects, and these QTL should represent genes that influence GPC independently from variation in the yield components. Such genes are of special interest in wheat breeding since they would allow an increase in GPC without a concomitant decrease in grain yield.

Relationships between grain protein content and grain yield components through quantitative trait locus analyses in a recombinant inbred line population derived from two elite durum wheat cultivars

Grain protein content (GPC) of durum wheat (Triticum turgidum L. var. durum) is an important trait for the nutritional value of grain and for influencing the technological property of flour. Protein content is a quantitative trait negatively correlated with grain yield, thus increase in protein quantity usually results in yield reduction. This study was initiated to introgress alleles for high GPC from var. dicoccoides into durum wheat germplasm by the backcross inbred line (BIL) method and to identify molecular markers linked to high GPC alleles not associated with depressing effects on yield. The backcross line 3BIL-85 with high GPC and similar grain yield to the recurrent parent was backcrossed to Latino, and the generations F2, F3 and F4 were evaluated for GPC and yield per spike (GYS) in three field trials. Three QTLs with major effects on GPC were detected on chromosome arms 2AS, 6AS and 7BL, identified by the markers Xcfa2164, XP39M37
 (250)
 and Xgwm577
 , respectively. Multiple regression analysis indicated that the three QTLs explained all the genetic variances of the trait. The high GPC parental line 3BIL-85 was not significantly different from the recurrent parent Latino for GYS, but the phenotypic correlation coefficient between GPC and GYS had negative values (from −0.02 to −0.28) in each trial, although it was statistically significant only in the F3 progeny trial. No co-located QTL for GYS was detected, excluding the hypothesis that the putative QTLs for GPC were indirect QTLs for low grain yield. The negative protein-yield response could be due to: (a) co-location of grain yield per spike QTLs with reduced phenotypic effects not detectable by the experimental design or statistical procedures, or to (b) opposite pleiotropic gene effects due to the major bio-energetic requirements for synthesis of protein then carbohydrates. Mapping loci by BILs should enable the production of near-isogenic lines in which the individual effects of each QTL can be examined in detail without confounding variations due to other putative QTLs.

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Detection of QTLs for grain protein content in durum wheat

Powdery mildew, caused by Blumeria graminis f.sp. tritici, is one of the most important wheat diseases in many regions of the world. Triticum turgidum var. dicoccoides (2n = 4x = AABB), the progenitor of cultivated wheats, shows particular promises as a donor of useful genetic variation for several traits, including disease resistances. The wild emmer accession MG29896, resistant to powdery mildew, was backcrossed to the susceptible durum wheat cultivar Latino, and a set of backcross inbred lines (BC5F5) was produced. Genetic analysis of F3 populations from two resistant introgression lines (5BIL-29 × Latino and 5BIL-42 × Latino) indicated that the powdery mildew resistance is controlled by a single dominant gene. Molecular markers and the bulked segregant analysis were used to characterize and map the powdery mildew resistance. Five AFLP markers (XP43M32
 (250), XP46M31
 (410), XP41M37
 (100), XP41M39
 (250), XP39M32
 (120)), three genomic SSR markers (Xcfd07, Xwmc75, Xgwm408) and one EST-derived SSR marker (BJ261635) were found to be linked to the resistance gene in 5BIL-29 and only the BJ261635 marker in 5BIL-42. By means of Chinese Spring nullisomic–tetrasomic, ditelosomic and deletion lines, the polymorphic markers and the resistance gene were assigned to chromosome bin 5BL6-0.29-0.76. These results indicated that the two lines had the same resistance gene and that the introgressed dicoccoides chromosome segment was longer (35.5 cM) in 5BIL-29 than that introgressed in 5BIL-42 (less than 1.5 cM). As no powdery mildew resistance gene has been reported on chromosome arm 5BL, the novel resistance gene derived from var. dicoccoides was designated Pm36. The 244 bp allele of BJ261635 in 5BIL-42 can be used for marker-assisted selection during the wheat resistance breeding process for facilitating gene pyramiding.

Molecular mapping of the novel powdery mildew resistance gene Pm36 introgressed from Triticum turgidum var. dicoccoides in durum wheat

Seed storage protein content of durum wheat (Triticum turgidum var. durum) has an important effect on nutritional value and pasta-making characteristics. The objective of this study was to determine by association with genetic markers the number, chromosomal location, and magnitude of effect of quantitative trait loci (QTLs) controlling protein concentration in kernels. A set of 65 recombinant inbred lines (RIs) was developed by single seed descent from a cross between cultivated durum wheat cv. ‘Messapia’ (low protein content) and accession MG4343 of the wild tetraploid wheat var. dicoccoides (high protein content). This population was characterized for eight morphological, six storage protein, one isozyme and 124 RFLP loci. Field trials were conducted in one location in 1993 and two locations in 1994. QTLs were mapped by regression analysis on each marker locus for each location and for the average across environments. A total of six putative QTLs were located on chromosome arms 4BS, SAL, 6AS, 6BS and 7BS. The number and size of QTLs detected varied across environments. The marker with the highest r2 value per QTL in each environment and across environments was chosen for a multiple linear regression analysis, which explained 49.2- 56.4% of the phenotypic variation for protein content. Only some of the markers were found to be negatively associated with plant grain yield and/or seed weight in one or two of the environments.

R. Simeone

Papers

A genetic linkage map of durum wheat

Relationships between grain protein content and grain yield components through quantitative trait locus analyses in a recombinant inbred line population derived from two elite durum wheat cultivars

Detection of QTLs for grain protein content in durum wheat

Molecular mapping of the novel powdery mildew resistance gene Pm36 introgressed from Triticum turgidum var. dicoccoides in durum wheat

Quantitative trait loci influencing grain protein content in tetraploid wheats