Cai X

Dundas IS

Faris JD

Friebe, BR

Gill, BS

Jin Y

Pumphrey MO

Qi LL

Xu SS

English

Sydney eScholarship

 1Chromosome engineering to enhance utility of alien-derived stem rust resistance  Xu SS1, Dundas IS2, Pumphrey MO3, Jin Y4, Faris JD1, Cai X5, Qi LL6, Friebe BR6, Gill BS6 1USDA-ARS Northern Crop Science Laboratory, Fargo, ND 58105, USA, 2School of Agriculture, Food and Wine, University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia, 3USDA-ARS Plant Science and Entomology Research Unit, Manhattan, KS 66506, USA, 4USDA-ARS Cereal Disease Laboratory, St. Paul, MN 55108, USA, 5Departments of Plant Sciences, North Dakota State University, Fargo, ND 58105, 6Wheat Genetic and Genomic Resources Center, Kansas State University, Manhattan, KS 66506, USA  ABSTRACT  In the past 50 years, a number of stem rust (Sr) resistance genes identified from wild relatives of wheat have been incorporated into wheat genomes through chromosome engineering.  Some of these genes, including Sr25, Sr26, Sr32, Sr37, Sr39, Sr40, Sr43, Sr44, SrR, and three unnamed novel Sr genes from Aegilops speltoides and Haynaldia villosa, are effective against Ug99. However, the alien chromosomal segments possess deleterious genes in addition to the Sr genes. To enhance the utility of these Sr genes in wheat breeding, we have been eliminating deleterious linkage drag associated with these Sr genes through homoeologous recombination. The ph1b mutant was used to induce recombination between the alien chromosomal segments and their homoeologs in wheat. Recombinants with reduced alien chromatin were identified and characterized through stem rust testing, molecular marker analysis, and fluorescent genomic in situ hybridization (FGISH). To date, several resistant lines with modified or shortened alien chromosomal segments have been developed.  Lines containing modified alien chromosome segments with genes SrR, Sr26, Sr32, and Sr39 are undergoing backcrossing and field evaluation for yield and quality characteristics in wheat breeding programs.  INTRODUCTION   Stem rust (caused by Puccinia graminis f.sp. tritici Eriks. & Henn.) is a serious disease of cultivated wheats, including durum (Triticum turgidum L. ssp. durum) and common wheat (T. aestivum L.). Deployment of resistance genes in commercial cultivars has provided effective control for the disease worldwide for decades. However, emergence of a new stem rust race, Ug99 (or TTKS) in Africa (8) and its spread to other areas has posed a serious threat to world wheat production because the race is virulent to most currently deployed Sr resistance genes (10). Thus, there is a need to identify and deploy Sr resistance genes that are effective against Ug99 into commercial wheat cultivars.   Cultivated wheats have a large number of relatives, which are useful sources of genes for wheat improvement. In the past 50 years, a number of Sr resistance genes identified in wheat relatives, such as Ae. speltoides, Thinopyrum ponticum, and rye (Secale cereale L.), have been incorporated into the wheat genomes through chromosome translocations. Some of these genes have been found to be highly effective against Ug99 (4, 10). However, most of the alien-derived Sr resistance genes are associated with deleterious linkage drag, which usually results in yield reduction and inferior quality (6).  Thus, they are virtually unusable in their current form.  To enhance the utility of Sr genes in wheat breeding, we have initiated work to eliminate the deleterious linkage drag associated with these Sr genes through homoeologous recombination. In this paper, we review sources of alien-derived stem rust resistance genes and describe our strategy and progress in improving several translocations.  STEM RUST RESISTANCE DERIVED FROM WILD RELATIVES OF WHEAT  Alien Stem Rust Resistance Genes Introgressed into Wheat Genomes Among 50 genes for stem rust resistance in wheat (7), 15 are derived from alien chromosomes of wheat relatives. Except for Sr31 (S. cereale), Sr34 (Ae. comosa), and Sr38 (Ae. ventricosa), 12 alien resistance genes were found to be effective against Ug99 (Table 1).    Table 1.  Alien species-derived stem rust (Sr) resistance genes that are effective against Ug99 (race TTKS).Gene Donor species Chro.1 IT2 Line Sr24 Th. ponticum 3DL L Agent/9*LMPG Sr25 Th. ponticum 7DL L Agatha/9*LMPG Sr26 Th. ponticum 6AL L EagleSr27 S. cereale 3A L 73,214,3-1/9*LMPG Sr32 Ae. speltoides 2A,2B L ER5155Sr36 T. timopheevi 2BS L W2691SrTt-1 Sr37 T. timopheevi 4BL L W3563 Sr39 Ae. speltoides 2B L RL6082Sr40 T. timopheevi 2BS L RL 6088 Sr43 Th. intermedium 7D L KS10-2 Sr44 Th. intermedium 7DS L Taf-2 SrR S. cereale 1D L DRA-1 1 Wheat chromosomes/arms involved in the translocations (7), 2 IT, infection type to race TTKS at seedling stage was based on Jin et al. (4) except for Sr43and SrR (unpublished data). Low infection types (L) are indicative of host resistance.   2 Potential Novel Sources of Stem Rust Resistance   In addition to the resistance genes listed in Table 1, we have identified a number of wheat-alien species derivatives with resistance to multiple stem rust races including Ug99 (Table 2). Among these derivatives, the Chinese Spring (CS)-H. villosa chromosome 6V disomic addition line, CS-Ae. speltoides 5S disomic addition line and Alcedo-Ae. caudata disomic addition line AIII should carry novel genes for stem rust resistance because none of the Sr genes currently available are derived from Ae. speltoides chromosome 5S,  H. villosa, and Ae. caudata.    Table 2. Potential novel sources of stem rust resistance from wild relative species of wheat.  Line and Pedigree 2n IT to Ug991 T. durum-Ae. speltoides translocation 28 L CS-H. villosa 6V addition 44 L CS-Ae. speltoides 5S addition 44 L T. aestivum cv. Alcedo 42 H AIII (Alcedo-Ae. caudata addition)  44 L Zhong 4 (T. aestivum/Th. intermedium) 56 L Zhong 5 (T. aestivum/Th. intermedium) 56 L Zhong 6 (T. aestivum/Th. intermedium) 56 L Zhong 7 (T. aestivum/Th. intermedium) 56 L Zhong 8 (T. aestivum/Th. intermedium) 56 L 78829 (T. aestivum/Th. intermedium) 56 L SS5 (T. aestivum/Th. ponticum) 56 L LDN/Ae. speltoides PI369581  41 L LDN/Ae. speltoides PI369600    42 L LDN/Ae. speltoides PI369609   42 L LDN 5D(5B)/Ae. speltoides PI393494  42 L LDN 5D(5B)/Ae. speltoides PI442448  42 L 1 IT, infection type at seedling stage was based on the unpublished data. Low infection types (L) are indicative of host resistance and high infection types (H) are indicative of host susceptibility.     The durum wheat-Ae. speltoides chromosome translocation line was originally developed by transferring an Sr gene from Ae. speltoides PI 369590 to stem rust-susceptible durum line 47-1 (L. R. Joppa, unpublished). The Sr gene has recently been determined to be located on a translocated 2B/2S chromosome using FGISH and molecular markers. The majority of the translocated chromosome is derived from Ae. speltoides 2S (J. D. Faris, S. S. Xu, and X. Cai, unpublished). Based on its reactions to multiple stem rust races, this resistance gene is different from Sr32 and Sr39, two Sr genes located on chromosome 2S of Ae. speltoides. This Ae. speltoides chromosomal fragment, therefore, may contain a novel stem rust resistance gene locus or allele.   Among the newly identified resistance lines, six wheat-Th. intermedium partial amphiploids (Zhong 4, Zhong 5, Zhong 6, Zhong 7, Zhong 8, and 78829),  one wheat-Th. ponticum partial amphiploid (SS5), three durum Langdon (LDN)-Ae. speltoides amphiploids, and two LDN 5D(5B)-Ae. speltoides amphiploids showed near-immunity or high levels of resistance to North American stem rust races and Ug99 (Table 2). These lines may provide additional novel genes for stem rust resistance.   ENHANCEMENT OF UTILITY OF ALIEN-DERIVED STEM RUST RESISTANCE VIA CHROMOSOME MANIPULATIONS   The common procedure for enhancing utility of alien-derived genes for desirable characters in wheat is to reduce the size of the alien segments by inducing new recombination between alien segments and wheat chromosomes. Generally, the smaller the alien chromatin, the more likely the translocation will have commercial value.  In our research, we are using the ph1b mutant and durum 5D(5B) substitutions to induce new translocations in hexaploid and tetraploid wheats, respectively.  Inducing Homoeologous Recombination in Hexaploid Wheat   For reducing the sizes of the alien chromatin carrying Sr32 Sr37, Sr39, Sr40, and Sr43 in hexaploid wheat, we used the previously described procedure (3, 9) that involves producing F2 populations from crosses between the translocation lines and CS ph1bph1b, followed by the use of molecular markers and FGISH to identify new translocation lines carrying the Sr genes. We have also used a modified procedure to improve efficiency for induction and identification of new translocations.  The F1 plants from crosses between the translocation lines and CS ph1bph1b are backcrossed to CS ph1bph1b plants and the remaining spikes are self-pollinated to produce F2’s.  The BC1F1 plants are evaluated for reaction to stem rust and genotyped at the Ph1 locus. The BC1F1 plants that are homozygous for ph1b and hemizygous for the alien segment are backcrossed to CS or elite stem rust-susceptible lines.   Then we evaluate the BC2 population for stem rust resistance. The resistant individuals selected from the population are characterized for the size of alien segments using FGISH and molecular markers.    Efforts to reduce the size of alien chromatins containing Sr32, Sr37, Sr39, Sr40, and Sr43 are currently underway in the two USDA-ARS laboratories in Manhattan, KS and Fargo, ND. To date, the F2 or BC1 populations derived from the original translocation stocks crossed with CS ph1bph1b have been developed. The University of Adelaide has developed several new lines with shortened alien chromatins carrying Sr genes SrR and Sr26 (1, 2).  Dundas et al. (2) also produced a number of lines with shortened or modified alien chromosome segments carrying Sr32, Sr37, Sr39, and Sr40 but used the ph1b mutant in a cv. Angas background. Lines containing modified alien chromosome segments with genes SrR, Sr26, Sr32, and  3Sr39 are undergoing backcrossing and field evaluation for yield and quality characteristics in wheat breeding programs in Australia. In the new line with SrR, the deleterious linkage drag affecting dough-quality appears to have been removed.  The gene Sr44 is currently available on a non-compensating translocation chromosome (T7DS-7Ai#1L·7Ai#1S).  The original 7Ai#1 disomic addition line (Vilmorin 27-DA 7Ai#1) has been crossed to CS monosomic for chromosome 7D (CS M7D) at USDA-ARS in Manhattan, KS. Double monosomic progeny of ‘CS M7D’/‘Vilmorin 27-DA 7Ai#1’ population are expected to produce compensating centromeric translocation lines among the F2 progeny.  A combination of molecular marker screening, cytology, and Sr disease screening will enable us to identify the compensating T7DL.7Ai#1S Robertsonian translocations with Sr44.  In addition, the resistant CS-Ae. speltoides 5S disomic addition line (CS-AESP DA 5S) was crossed with CS monosomic for chromosome 5D (CS M5D), and similarly the resistant CS-H. villosa 6V disomic addition line (CS-HVIL DA 6V) has been hybridized with CS monosomic for chromosome 6D (CS M6D).  The ‘CS M5D’/’ CS-AESP DA 5S’ and ‘CS M6D’/’CS-HVIL DA 6V’ populations have been characterized as outlined above in order to identify stem rust-resistant compensating translocations. A second round of chromosome engineering using ph1b-induced homoeologous recombination is underway to further reduce the size of the alien chromosome segments and reduce linkage drag.   Inducing Homoeologous Recombination in Tetraploid Wheat   Homoeologous pairing can be induced in aneuploids nullisomic for chromosome 5B. Durum lines Rusty and 47-1 are near-universally susceptible to stem rust races (5) and their 5D(5B) substitution lines are currently available for inducing crossing-over of homoeologous chromosomes in tetraploid wheat. Thus, shortening the size of the alien segment in the durum-Ae. speltoides translocation line is being performed using the Rusty and 47-1 5D(5B) substitution lines.  The crossing and testing procedure is similar to that for hexaploid wheat.  Currently, the durum-speltoides line has been crossed to Rusty 5D(5B) double monosomic and to the 47-1 5D(5B) disomic substitution at USDA-ARS in Fargo, ND.  The double-monosomic (13’’ + 2’) hybrid plants have been backcrossed to their respective parent (ie. Rusty 5D(5B) and 47-1 5D(5B) disomic substitutions). In the coming season, the BC1 plants will be tested for resistance to stem rust.  The resistant BC1 plants will then be screened using the molecular markers for the Ph1 locus. The resistant plants nullisomic for chromosome 5B will be backcrossed to Rusty.  Similar to transfers in hexaploid wheat, the hybrids would initially be tested for stem rust resistance followed by molecular marker analysis. Any plants identified as having a reduced alien segment would be examined by FGISH to verify a reduced alien segment size.    The development and selection of translocation stocks is usually a slow process. However, the availability of various cytogenetic stocks and modern molecular techniques make the implementation of the research more feasible and efficient than ever before.  As a part of a global cooperative effort in confining the Ug99 threat, the new lines with eliminated or reduced deleterious drag, once they become available, will be used to develop superior wheat cultivars/germplasm adapted to various environments.  REFERENCES  1. Anugrahwati DR, Shepherd WK, Verlin CD, Zhang P, Mirzaghaderi G, Walker E, Francki GM, and Dundas SI (2008) Isolation of wheat-rye 1RS recombinants that break the linkage between the stem rust resistance gene SrR and secalin. Genome 51:341-349. 2. Dundas IS, Anugrahwati DR, Verlin DC, Park RF, Bariana HS, Mago R, and Islam AKMR (2007) New sources of rust resistance from alien species: meliorating linked defects and discovery. Aust J Agric Res 58:545–549. 3. Friebe B, Jiang J, Raupp WJ, McIntosh R, and Gill BS (1996) Characterization of wheat-alien translocations conferring resistance to diseases and pests: current status.  Euphytica 91:59-87. 4. Jin Y, Singh RP, Ward RW, Wanyera R, Kinyua M, Njau P, Fetch T, Pretorius ZA, and Yahyaoui A (2007) Characterization of seedling infection types and adult plant infection responses of monogenic Sr gene lines to race TTKS of Puccinia graminis f. sp. tritici. Plant Dis 91:1096-1099. 5. Klindworth DL, Miller JD, and Xu SS (2006) Registration of Rusty durum wheat. Crop Sci 46:1012-1013. 6. Lukaszewski AJ (2000) Manipulation of the 1RS.1BL translocation in wheat by induced homoeologous recombination. Crop Sci 40:216-225. 7. McIntosh, RA, Yamazaki Y, Devos KM, Dubcovsky J, Rogers J, Appels R (2005) Catalogue of gene symbols for wheat. MacGene 2005 (http://www.grs.nig.ac.jp/wheat/komugi/genes/download.jsp, verified June 24, 2008). 8. Pretorius ZA, Singh RP, Wagoire WW, Payne TS (2000) Detection of virulence to wheat stem rust resistance gene Sr31 in Puccinia graminis. f. sp. tritici in Uganda. Plant Dis 84:203. 9. Qi L, Friebe B, Zhang P, and Gill BS (2007) Homoeologous recombination, chromosome engineering and crop improvement.  Chrom Res 15:3-19. 10. Singh RP, Hodson DP, Jin Y, Huerta-Espino J, Kinyua MG, Wanyera R, Njau P, and Ward RW (2006) Current status, likely migrations and strategies to mitigate the threat to wheat production from race Ug99 (TTKS) of stem rust pathogen. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources, 2006, 1, No. 054, 13 pp. 

Chromosome engineering to enhance utility of alien-derived stem rust resistance

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Chromosome engineering to enhance utility of alien-derived stem rust resistance

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