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Frontiers of Agricultural Science and Engineering

Front. Agr. Sci. Eng.    2019, Vol. 6 Issue (3) : 210-224     https://doi.org/10.15302/J-FASE-2019268
REVIEW
Progress in breeding for resistance to Ug99 and other races of the stem rust fungus in CIMMYT wheat germplasm
Sridhar BHAVANI1(), David P. HODSON1, Julio HUERTA-ESPINO1,2, Mandeep S. RANDHAWA3, Ravi P. SINGH1
1. International Maize and Wheat Improvement Center, Texcoco 56237, Mexico
2. Campo Experimental Valle de México INIFAP, Chapingo 56230, Mexico
3. International Maize and Wheat Improvement Center, ICRAF Campus, Nairobi 00100, Kenya
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Abstract

Races belonging to the Ug99 (TTKSK) lineage of the wheat stem rust fungus, carrying complex virulence combinations, and their migration to countries in Africa, Middle East and Asia continue to pose a significant threat to global wheat production. The rapid spread of additional races, e.g., TKTTF or the Digalu lineage, in several countries causing localized epidemics reminds us of the vulnerability of wheat germplasm to stem rust disease, a formidable foe referenced as early as biblical times. A global rust monitoring system reflecting increased surveillance efforts has identified 13 races within the Ug99 lineage in 13 countries and unrelated lineages are emerging, spreading and posing serious threats to wheat production. Race TKTTF has caused localized epidemics in Ethiopia and its variants have been recently implicated in stem rust outbreaks in Europe. Concerted research efforts have resulted in the identification of several new resistance genes and gene combinations for use in breeding. Combining multiple adult plant resistance (APR) genes in high-yielding backgrounds and discovery of new quantitative trait loci conferring stem rust resistance has progressed in the recent years, enhancing the durability of resistance. Effective gene stewardship and new generation breeding materials and cultivars that combine multiple race-specific or minor to intermediate effect APR genes, complemented by active surveillance and monitoring, have helped to limit major epidemics and increase grain yield potential in key target environments.

Keywords adult plant resistance      black rust      race-specific resistance      Triticum aestivum     
Corresponding Authors: Sridhar BHAVANI   
Just Accepted Date: 06 June 2019   Online First Date: 17 July 2019    Issue Date: 26 July 2019
 Cite this article:   
Sridhar BHAVANI,David P. HODSON,Julio HUERTA-ESPINO, et al. Progress in breeding for resistance to Ug99 and other races of the stem rust fungus in CIMMYT wheat germplasm[J]. Front. Agr. Sci. Eng. , 2019, 6(3): 210-224.
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http://journal.hep.com.cn/fase/EN/10.15302/J-FASE-2019268
http://journal.hep.com.cn/fase/EN/Y2019/V6/I3/210
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Sridhar BHAVANI
David P. HODSON
Julio HUERTA-ESPINO
Mandeep S. RANDHAWA
Ravi P. SINGH
Fig.1  Detection and distribution of Puccinia graminis tritici races belonging to Ug99 race group in 2019. Updated from Singh et al.[25]
Race1 Common alias Resistance genes and avirulence (A) or virulence (V) status Confirmed countries (year detected)
Sr31 Sr21 Sr24 Sr36 Sr9h SrTmp
TTKSK Ug99 V V A A A A Uganda (1998), Kenya (2001), Ethiopia (2003), Sudan (2006), Yemen (2006), Iran (2007), Tanzania (2009), Eritrea (2012), Rwanda (2014), Egypt (2014)
TTKSF A V A A A A South Africa (2000), Zimbabwe (2009), Uganda (2012)
TTKST Ug99+ Sr24 V V V A A A Kenya (2006), Tanzania (2009), Eritrea (2010), Uganda (2012)
TTTSK Ug99+ Sr36 V V A V A A Kenya (2006), Tanzania (2009), Ethiopia (2010), Uganda (2012), Rwanda (2014), Egypt (2014)
TTKSP A V V A A A South Africa (2007)
PTKSK V A A A A A Kenya (2009), Ethiopia (2007), Yemen (2009), South Africa (2017)
PTKST V A V A A A Ethiopia (2007), Kenya (2008), South Africa (2009), Eritrea (2010), Mozambique (2010), Zimbabwe (2010)
TTKSF+ A V A A V A South Africa (2010), Zimbabwe (2010)
TTKTT Ug99+ Sr24 + SrTmp V V V A A V Kenya (2014)
TTKTK Ug99+ SrTmp V V A A A V Kenya (2014), Egypt (2014), Eritrea (2014), Rwanda (2014), Uganda (2014)
TTHSK V V A A A A Kenya (2014)
PTKTK V A A A A A Kenya (2014)
TTHST V V V A A A Kenya (2013)
Tab.1  Puccinia graminis tritici races belonging to Ug99 lineage identified until 2019 in various countries with avirulence/virulence status on discriminating resistance genes updated(Updated from Singh et al.[25])
Fig.2  Wheat accessions phenotyped during 2005–2018 for Ug99 resistance at Njoro (Kenya) and participating countries, in partnership with Kenya Agriculture Livestock Research Organization, Kenya
Gene Reported linked marker Marker type Reference stock Reference
Sr13 barc104, dupw167, CD926040, BE471213 SSR Kofa, Kronos [42]
Sr22 wmc633, cfa2123 SSR Sr22Tb, Steinwedel [43]
Sr23 Xgwm210 SSR AC Domain [44]
Sr25 wMAS000032, wmc221 SSR Agatha, Misr#1 [45]
Sr26 Sr26#43, BE518379 STS WA1 [46]
Sr32 csSr32#1, csSr32#2 STS Angas, Aroona, Westonia [47]
Sr33 barc152, cfd15, BE405778, BE499711 SSR RL5288 [48,49]
Sr35 cfa2170, cfa2076, wmc169, wmc559 SSR G2919 [50]
Sr38 CIMwMAS0004, Ventriup/LN2 SNP, STS VPM1 [51]
Sr42 barc183, FSD_RSA SSR Norin 40 [52]
Sr47 Xrwgs38 SSR DAS15 [53]
Sr50 Sr50-5p-F3/R2 SSR Gabo1BL.1RS and Gabo1DL.1RS-DR.A [54]
Sr-6DS gpw5182, cfd49 SSR Niini, Coni, Blouk [55]
SrND643 Xgwm350, Xwmc219 SSR ND643 [56]
SrHuw234 wmc332 SSR Huwa [53]
SrYanac barc200 SSR Yaye [53]
Tab.2  Molecular markers linked to stem rust resistance genes conferring seedling resistance and widely used in CIMMYT breeding program
Gene Reported linked marker Marker type Reference stock Reference
Lr34/Yr18/Pm38/Sr57 wMAS000003, wMAS000004 STS, SNP Parula, Thatcher, Glenlea, Jupateco R, Opata, Bezostaya, Chinese Spring. [75]
Lr46/Yr29/Pm39/Sr58 csLV46, csLV46G22 CAPS Pavon 76, Parula, [76]
Lr67/Yr46/Pm46/Sr55 csSNP856 SNP RL6077 [77]
Sr2/Yr30 csSr2, wMAS000005 CAPS Pavon76 [78]
Tab.3  Molecular markers for pleotropic adult plant resistance (APR) genes used in CIMMYT wheat breeding program
Germplasm identification no. Cross name/Pedigree Selection history Stem rust severity/% Resistance genes/ Category1
8237333 BECARD/ND643/2*WBLL1/3/SWSR22T.B./2*BLOUK #1//WBLL1*2/KURUKU CMSS13Y00149S-099Y-099M-099NJ-099NJ-8Y-0WGY 5 Sr22/SrND643
8234886 MISR 1/3/SWSR22T.B./2*BLOUK #1//WBLL1*2/KURUKU CMSS13B00039S-099M-099NJ-099NJ-10Y-0WGY 15 Sr25/Sr22
8235073 ND643/2*WBLL1/4/WHEAR/KUKUNA/3/C80.1/3*BATAVIA//2*WBLL1/5/BORL14 CMSS13B00139S-099M-099NJ-099NJ-50Y-0WGY 5 Sr25/SrND643
8235528 WBLL1*2/BRAMBLING*2//BAVIS/3/SWSR22T.B./2*BLOUK #1//WBLL1*2/KURUKU CMSS13B00381S-099M-099NJ-099NJ-5Y-0WGY 5 Sr22/Sr13
8235657 KRONSTAD F2004/KENYA SUNBIRD//WHEAR/KRONSTAD F2004/3/WBLL1*2/BRAMBLING*2//BAVIS CMSS13B00453S-099M-099NJ-099NJ-25Y-0WGY 10 Sr13/SrND643
8236725 DANPHE #1*2/SHORTENED SR26 TRANSLOCATION/3/SWSR22T.B./2*BLOUK #1//WBLL1*2/KURUKU/4/SWSR22T.B./2*BLOUK #1//WBLL1*2/KURUKU CMSS13B01575T-099TOPY-099M-099NJ-099NJ-2Y-0WGY 10 Sr22/Sr26
8236942 MUTUS*2//ND643/2*WBLL1/3/2*SWSR22T.B./KACHU//2*KACHU CMSS13B01701T-099TOPY-099M-099NJ-099NJ-29Y-0WGY 1 Sr22/SrND643
8236956 WHEAR/KUKUNA/3/C80.1/3*BATAVIA//2*WBLL1*2/4/NIINI #1*2/5/SWSR22T.B./2*BLOUK #1//WBLL1*2/KURUKU CMSS13B01707T-099TOPY-099M-099NJ-099NJ-14Y-0WGY 5 SrNini/Sr22
8236960 SWSR22T.B./FRANCOLIN #1//2*FRNCLN/5/WHEAR/KUKUNA/3/C80.1/3*BATAVIA//2*WBLL1*2/4/NIINI #1/6/BORL14 CMSS13B01709T-099TOPY-099M-099NJ-099NJ-11Y-0WGY 5 Sr22/SrNini
8248316 WBLL1*2/BRAMBLING//TAM200/TUI/3/VILLA JUAREZ F2009/4/2*BORL14 CMSS13B01705T-099TOPY-099M-099NJ-099NJ-9Y-0RGY 5 Sr1A.1R
8249245 BABAX/LR42//BABAX/3/ER2000/4/BAVIS/5/SWSR22T.B./2*BLOUK #1//WBLL1*2/KURUKU CMSS14Y00716S-099Y-099M-0SY-19M-0RGY 10 Sr13/Sr22
8238251 KFA/2*KACHU/3/2*ATTILA*2/PBW65*2//MURGA CMSS13Y01093T-099TOPM-099Y-099M-099NJ-099NJ-18Y-0WGY 5 APR_NIR
8238893 TOB/ERA//TOB/CNO67/3/PLO/4/VEE#5/5/KAUZ/6/FRET2/7/PASTOR//MILAN/KAUZ/3/BAV92/8/ATTILA*2/PBW65*2//TNMU/9/ATTILA*2/PBW65*2//MURGA CMSS13Y01437T-099TOPM-099Y-099M-099NJ-099NJ-32Y-0WGY 5 APR_NIR
8239063 CORRELL/3/PBW343*2/KUKUNA//TECUE #1/4/PBW343*2/KUKUNA*2//FRTL/PIFED CMSS13Y01496T-099TOPM-099Y-099M-099NJ-099NJ-19Y-0WGY 10 APR_R
8234995 KACHU/DANPHE//KFA/2*KACHU CMSS13B00105S-099M-099NJ-099NJ-41Y-0WGY 10 APR_R
8235423 KACHU//KIRITATI/2*TRCH/3/KFA/2*KACHU CMSS13B00118S-099M-099NJ-099NJ-8Y-0WGY 5 APR_NIR
8235262 SUP152/2*DANPHE #1//BORL14 CMSS13B00270S-099M-099NJ-099NJ-6Y-0WGY 10 APR_R
8235936 BECARD//ND643/2*WBLL1/3/KACHU/DANPHE CMSS13B00700S-099M-099NJ-099NJ-5Y-0WGY 5 APR_NIR
8236909 WHEAR/KUKUNA/3/C80.1/3*BATAVIA//2*WBLL1/4/PAURAQUE #1/5/WHEAR/KUKUNA/3/C80.1/3*BATAVIA//2*WBLL1/6/2*KACHU/DANPHE CMSS13B01680T-099TOPY-099M-099NJ-099NJ-14Y-0WGY 5 APR_NIR
8236918 CHYAK1/VILLA JUAREZ F2009//WBLL1*2/BRAMBLING/7/PRL/2*PASTOR/4/CHOIX/STAR/3/HE1/3*CNO79//2*SERI/5/KIRITATI/2*TRCH/6/PRL/2*PASTOR/4/CHOIX/STAR/3/HE1/3*CNO79//2*SERI/8/KACHU/DANPHE CMSS13B01683T-099TOPY-099M-099NJ-099NJ-10Y-0WGY 10 APR_R
8236943 SUP152*2/TINKIO #1/4/FRET2*2/SHAMA//KIRITATI/2*TRCH/3/BAJ #1/5/SUP152*2/TINKIO #1 CMSS13B01703T-099TOPY-099M-099NJ-099NJ-15Y-0WGY 5 APR_NIR
8244588 KACHU/SAUAL/3/TACUPETO F2001/BRAMBLING//KIRITATI/4/COPIO CMSS14Y00648S-099Y-099M-0SY-13M-0WGY 5 APR_NIR
8245010 KACHU/DANPHE*2//BORL14 CMSS14Y01482T-099TOPM-099Y-099M-0SY-24M-0WGY 15 APR_R-MR
8245012 KACHU/DANPHE*2//BORL14 CMSS14Y01482T-099TOPM-099Y-099M-0SY-34M-0WGY 5 APR_NIR
8241262 KACHU/BECARD//WBLL1*2/BRAMBLING*2/5/ATTILA/3*BCN*2//BAV92/3/KIRITATI/WBLL1/4/DANPHE CMSS14B01373T-099TOPY-099M-0SY-37M-0WGY 10 APR_R
8248604 CHIPAK*2//TRCH/HUIRIVIS #1 CMSS13Y01097T-099TOPM-099Y-099M-099NJ-099NJ-6Y-0RGY 5 APR_NIR
8249240 NGL/4/PFAU/MILAN/3/BABAX/LR42//BABAX/5/KFA/2*KACHU CMSS14Y00712S-099Y-099M-0SY-5M-0RGY 5 APR_NIR
Tab.4  CIMMYT wheat germplam combining high yield and stem rust resistance (R, APR categories) in international nurseries (based on highest disease severity recorded in four seasons of field-testing at KALRO, Njoro, Kenya and seedling tests)
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