Marker Assisted Selection in Wheat Marker Assisted Selection in Wheat - HOME CSREES-USDA

Quality traits. Pre-harvest sprouting tolerance (PHS)

Contributed by Mark Sorrells (


1. RFLP analysis of genomic regions associated with resistance to preharvest sprouting in wheat.. Anderson, J. A.; Sorrells, M. E.; Tanksley, S. D. In: Crop Science, 1993, 33 (3): 453-459

Resistance to preharvest sprouting (PHS) is difficult to incorporate into new varieties because heritability is low and selection is limited to one generation per year. Our objective was to identify genomic regions containing quantitative trait loci (QTL) associated with resistance to PHS in two recombinant inbred (R) populations of white wheat (Triticum aestivum L. em. Thell.) by restriction fragment length polymorphism (RFLP) markers. One population consisted of 78 RI lines from the cross of NY6432-18 (NY18) times 'Clark's Cream' (CC). The second population consisted of 138 RI lines from the cross between sib lines NY18 and NY6432-10 (NY10). The NY18/CC and NY18/10 populations, were evaluated for PHS in six and seven environments, respectively, by examining physiologically mature spikes under simulated rainfall. The three parental lines were surveyed for polymorphism with 195 low-copy RFLP clones. Individual RI lines from the NY18/CC and NY18/NY10 populations were probed with 37 and 27 polymorphic clones, respectively. Eight regions of the genome (four from each population) were significantly associated with resistance to PHS. Based on multiple regression, specific sets of markers and their interactions accounted for 44% of the genetic variance for PHS in the NY18/CC and 51% in the NY18/NY10 populations. These markers could find utility in breeding programs as indirect selection criteria for improvement of PHS resistance.

Back to PHS Main Page     Back to top

2. Inheritance in synthetic hexaploid wheat 'RSP' of sprouting tolerance derived from Aegilops tauschii Cosson. Xiu-Jin, L.; Deng-Cai, L.; Zhi-Rong, W. In: Euphytica, 1997, 95(3):321-323

An artificial amphiploid 'RSP' (2n = 42, AABBDD) between tetraploid landrace Ailanmai (Triticum turgidum L., 2 = 28, AABB) and Aegilops tauschii (DD, 2n = 14) expressed high tolerance to preharvest sprouting which derived from Aegilops tauschii. To determine the inheritance of sprouting tolerance in 'RSP', it was crossed with six cultivars which vary in susceptibility to preharvest sprouting. Preharvest sprouting tolerance was assessed on F-2 plants using germination towels. Preharvest sprouting tolerance was inherited as a recessive trait which was controlled by one gene.

Back to PHS Main Page     Back to top

3. Genetic analysis of preharvest sprouting tolerance in three wheat crosses.  Lawson, W. R.; Godwin, I. D.; Cooper, M.; Brennan, P. S. In: Australian Journal of Agricultural Research, 1997, 48(2):215-221

Three recombinant inbred populations were assessed for tolerance to preharvest sprouting (PHS). Genetic analysis of the PHS scores, as assessed under artificial rain treatment, indicated that for 2 of the populations, tolerance to sprouting was simply inherited and was controlled by 2 independent genes, both of which are necessary for full tolerance. The data presented here show that in these 2 populations the trait is highly heritable under controlled environment situations. It was also demonstrated that the red seed colour gene, derived from Aus1490 and traditionally associated with tolerance, is not necessary for full tolerance to sprouting, although indirect selection for preharvest sprouting tolerance can be performed very effectively by selecting for red grain. The presence of white-seeded lines, recovered from this cross with a red-seeded donor of PHS tolerance, that axe at least as tolerant as the most tolerant red-seeded individuals demonstrates that red-seeded donors of PHS tolerance should not be discarded for improvement of this trait.

Back to PHS Main Page     Back to top

4. Identification of a microsatellite on chromosomes 6B and a STS on 7D of bread wheat showing an association with preharvest sprouting tolerance. Roy, J.K.; Prasad, M.; Varshney, R.K.; Balyan, H.S.; Blake, T.K.; Dhaliwal, H.S.; Singh, H; Edwards, K.J.; Gupta, P.K.In: Theoretical & Applied Genetics, 1999, 99(1-2):336-340.

In bread wheat, the transfer of tolerance to preharvest sprouting (PHS) that is associated with genotypes having red kernel colour to genotypes with amber kernels is difficult using conventional methods of plant breeding. The study here was undertaken to identify DNA markers linked with tolerance to PHS as these would allow indirect marker-assisted selection of PHS-tolerant genotypes with amber kernels. For this purpose, a set of 100 recombinant inbred lines (RILs) was developed using a cross between a PHS-tolerant genotype, SPR8198, with red kernels and a PHS-susceptible cultivar, 'HD2329', with white kernels. The two parents were analysed with 232 STMS (sequence-tagged microsatellite site) and 138 STS (sequence-tagged site) primer pairs. A total of 300 (167 STMSs and 133 STSs) primer pairs proved functional by giving scorable PCR products. Of these, 57 (34%) STMS and 30 (23%) STS primer pairs detected reproducible polymorphism between the parent genotypes. Using these primer pairs, we carried out bulked segregant analysis on two bulked DNAs, one obtained by pooling DNA from 5 PHS-tolerant RILs and the other similarly derived by pooling DNA from 5 PHS-susceptible RILs. Two molecular markers, 1 STMS primer pair for the locus wmc104 and a STS primer pair for the locus MST101, showed apparent linkage with tolerance to PHS. This was confirmed following selective genotyping of individual RILs included in the bulks. Chi-square contingency tests for independence were conducted on the cosegregation data collected on 100 RILs involving each of the two molecular markers (wmc104 and MST101) and PHS. The tests revealed a strong association between each of the markers and tolerance to PHS. Using nullisomic-tetrasomic lines, we were able to assign wmc104 and MST101 to chromosomes 6B and 7D, respectively. The results also indicated that the tolerance to PHS in SPR8198 is perhaps governed by two genes (linked with two molecular markers) exhibiting complementary interaction.

Back to PHS Main Page     Back to top

5. Genetic map locations for orthologous Vp1 genes in wheat and rice.. Bailey, P. C.; McKibbin, R. S.; Lenton, J. R.; Holdsworth, M. J.; Flintham, J. E.; Gale, M. D. In: Theoretical and Applied Genetics, 1999, 98(2):281-284.

Chromosome locations for gene orthologues of the dormancy-related maize transcription factor VIVIPAROUS-1, encoded by the Vp1 locus on maize chromosome 3, were determined in wheat (Triticum aestivum L.) and rice (Oryza sativa L.) via linkage to markers on existing molecular maps using a cDNA of a wheat Vp1 orthologue as a probe in genomic Southern analyses. Vp1-orthologous loci were detected on the long arms of wheat chromosomes 3A, 3B and 3D (Xlars10 (taVp1) loci) and rice chromosome 1 (osVp1), in line with previous evidence of synteny between these regions of the rice and wheat genomes and chromosome 3 of maize. The wheat loci mapped some 30 cM from the centromeres and some 30 cM proximal to the red grain (R) loci that control seed colour and coat-imposed dormancy. This unequivocal, genetic separation of the Vp1 and R loci may offer an opportunity for improving resistance to pre-harvest sprouting in wheat

Back to PHS Main Page     Back to top

6. Genetic analysis of pre-harvest sprouting resistance in a wheat X spelt cross. . Zanetti, S.; Winzeler, M.; Keller, M.; Keller, B.; Messmer, M. In: Crop Science, 2000, 40(5):1406-1417.

Breeding for pre-harvest sprouting (PHS) resistance in wheat (Triticum aestivum L.) and spelt (Triticum spelta L.) is difficult because PHS is quantitatively inherited and strongly affected by environmental factors. The aim of this study was to detect molecular markers linked to quantitative trait loci (QTL) involved in PHS resistance to improve the breeding process. We measured falling number (FN) and alpha-amylase activity (AA) of 226 F5 recombinant inbred lines (RILs) originating from a cross between the Swiss wheat cultivar Forno and the Swiss spelt cultivar Oberkulmer in four environments. QTL analysis was performed with 204 RILs and based on a genetic map of 183 loci. Across environments, 12 and 13 QTL were detected for FN and AA, respectively. Altogether the QTL explained more than 75% of the phenotypic variance. The two traits were highly correlated (r = -0.91) and of the 13 QTL for AA, nine coincided with QTL for FN. Three of the six QTL with major effects (R2 gtoreq 15%) on PHS resistance coincided with QTL for ear length. The QTL with the strongest impact had the positive allele from Oberkulmer and was located on 5AL at the q locus, which is responsible for the typical ear morphology of spelt. The QTL on 6A (with the positive allele from Forno), 3B, and 7B (both with the positive allele from Oberkulmer) improve PHS resistance without changing the ear morphology. Thus, these QTL could be important for marker assisted selection for PHS resistance in both the wheat and the spelt germplasm.

Back to PHS Main Page     Back to top

7. Detection of loci controlling seed dormancy on group 4 chromosomes of wheat and comparative mapping with rice and barley genomes.. Kato, K; Nakamura, W; Tabiki, T; Miura, H; Sawada, S. In: Theoretical & Applied Genetics, 2001, 102(6-7):980-985.

Three quantitative trait loci (QTLs) controlling seed dormancy were detected on group 4 chromosomes of wheat (Triticum aestivum L.) using 119 doubled haploid lines (DHLs) derived from a cross between AC Domain and Haruyutaka. A major QTL, designated QPhs.ocs-4A.1, was identified within the marker interval between Xcdo795 and Xpsr115 in the proximal region of the long arm of chromosome 4A. Two minor QTLs, QPhs.ocs-4B.2 on 4B and QPhs.ocs-4D.2 on 4D, were flanked by common markers, Xbcd1431.1 and Xbcd1431.2 in the terminal region of the long arms, suggesting a homoeologous relationship. These three QTLs explained more than 80% of the total phenotypic variance in seed dormancy of DHLs grown in the field and under glasshouse conditions. The AC Domain alleles at the three QTLs contributed to increasing seed dormancy. Comparative maps across wheat, barley and rice demonstrated the possibility of a homoeologous relationship between QPhs.ocs-4A.1 and the barley gene SD4, while no significant effects of the chromosome regions of wheat and barley orthologous to rice chromosome 3 region carrying a major seed dormancy QTL were detected.

Back to PHS Main Page     Back to top

8. Integrated physical maps of 2DL, 6BS and 7DL carrying loci for grain protein content and pre-harvest sprouting tolerance in bread wheat. Varshney, R.K.; Prasad, M.; Roy, J.K.; Roeder, M.S.; Balyan, H.S.; Gupta, P.K. In: Cereal Research Communications, 2001, 29(1-2):33-40.

In our two earlier studies on bread wheat, we identified three molecular marker loci - one (Xwmc41) associated with grain protein content (GPC) was located on 2DL and the other two (Xwmc104 and Xmst101) associated with pre-harvest sprouting tolerance (PHST) were located one each on 6BS and 7DL. These studies were extended using additional marker loci already known to be located on these arms. Seven STMS marker loci, that were already mapped on 2DL (Roder et al., 1998a), and 13 STMS marker loci that were already mapped on 6BS and 7DL were tested for possible genetic association with GPC/PHST. Although, some of these markers did show polymorphism between the contrasting parents, none of them showed linkage with GPC/ PHST or with the markers associated with them. This encouraged us to undertake physical mapping of all the loci known to be located on 2DL, 6BS and 7DL. The marker loci and the regions to which they were mapped included the following: (i) Xwmc41 (an STMS locus), that was associated with a QTL for GPC, was assigned to the terminal 0.24 fraction of 2DL; (ii) from among two molecular marker loci associated with PHST, Xwmc104 (an STMS locus) was assigned to terminal 0.76 fraction of the 6BS satellite and Xmst101 (an STS locus) was assigned to proximal centromeric 0.10 fraction of 7DL; (iii) 13 STMS marker loci, earlier genetically mapped on 6BS and 7DL, were also assigned to specific physical regions of these two arms. The marker loci that were physically mapped during the present study were integrated with those earlier mapped in a similar way, and integrated physical maps with 27 marker loci on 2DL, 42 marker loci on 6BS and 54 marker loci on 7DL were prepared. We believe that these integrated physical maps should prove useful for a variety of studies in future.

Back to PHS Main Page     Back to top

9. Mapping quantitative trait loci associated with variation in grain dormancy in Australian wheat. . Mares, D.J.; Mrva, K. In: Australian Journal of Agricultural Research, 2001, 52(11-12):1257-1265.

Preharvest sprouting is a problem in many regions of the world, resulting in downgrading of quality, substantial economic losses to wheat growers, and difficulties for grain handling and marketing agencies. Improvements in tolerance from the introduction of better grain dormancy at, or near, harvest-ripeness would be expected to have a significant impact on the incidence and severity of sprouting. Intermediate levels of dormancy in older Australian wheats, such as Halberd, and a small number of current cultivars could be used in the short term while more extreme dormancy is being introgressed into locally adapted germplasm. A doubled haploid population derived from Cranbrook (extremely non-dormant, very susceptible to sprouting) X Halberd (intermediate dormancy, moderately tolerant to preharvest sprouting) was grown in replicated experiments and ripe grain harvested for assessment of dormancy, measured as a germination index. Consistent differences were observed between the parents in both experiments. For the bulk of the progeny, the germination index fell within a range defined by Cranbrook at the upper and Halberd at the lower end. Significant quantitative trait loci, all contributed by the very susceptible parent, that explained 11%, 9%, and 9% of the phenotypic variation were identified on chromosome arms 2AL, 2DL, and 4AL, respectively. These QTLs offer the opportunity to develop molecular markers for grain dormancy and to develop a better understanding of the mechanisms involved in this trait.

Back to PHS Main Page     Back to top

10. Study of the relationship between pre-harvest sprouting and grain color by quantitative trait loci analysis in a white X red grain bread-wheat cross.. Groos, C.; Gay, G.; Perretant, M.-R.; Gervais, L.; Bernard, M.; Dedryver, F.; Charmet, G. In: Theoretical and Applied Genetics, 2002, 104(1):39-47.

In many wheat (Triticum aestivum L.) growing areas, pre-harvest sprouting (PHS) may cause important damage, and in particular, it has deleterious effects on bread-making quality. The relationship between PHS and grain color is well known and could be due either to the pleiotropic effect of genes controlling red-testa pigmentation (R) or to linkage between these genes and other genes affecting PHS. In the present work, we have studied a population of 194 recombinant inbred lines from the cross between two cultivars, 'Renan' and 'Recital', in order to detect QTLs for both PHS resistance and grain color. The variety 'Renan' has red kernels and is resistant to PHS, while 'Recital' has white grain and is highly susceptible to PHS. A molecular-marker linkage map of this cross was constructed using SSRs, RFLPs and AFLPs. The population was evaluated over 2 years at Clermont-Ferrand (France). PHS was evaluated on mature spikes under controlled conditions and red-grain color was measured using a chromameter. Over the 2 years, we detected four QTLs for PHS, all of them being co-localized with QTLs for grain color. Three of them were located on the long arm of chromosomes 3 A, 3B and 3D, close to the loci where the genes R and taVp1 were previously mapped. For these three QTLs, the resistance to PHS is due to the allele of the variety 'Renan'. Another co-located QTL for PHS and grain color was detected on the short arm of chromosome 5 A. The resistance for PHS for this QTL is due to the allele of 'Recital'.

Back to PHS Main Page     Back to top

11. Development and validation of a Viviparous-1 STS marker for pre-harvest sprouting tolerance in Chinese wheats.. Yang Y, Zhao XL, Xia LQ, Chen XM, Xia XC, Yu Z, He ZH, Röder M. In: Theoretical and Applied Genetics, 2007, 115(7):971-980. DOI: 10.1007/s00122-007-0624-z

Pre-harvest sprouting (PHS) of wheat reduces the quality of wheat grain, and improving PHS tolerance is a priority in certain wheat growing regions where conditions favorable for PHS exist. Two new Viviparous-1 allelic variants related to PHS tolerance were investigated on B genome of bread wheat, and designated as Vp-1Bb and Vp-1Bc, respectively. Sequence analysis showed that Vp-1Bb and Vp-1Bc had an insertion of 193-bp and a deletion of 83-bp fragment, respectively, located in the third intron region of the Vp-1B gene. The insertion and deletion affected the expression level of the Vp1 at mature seed stage, more correctly spliced transcripts were observed from the genotypes with either insertion or deletion than that of the wild type. Based on these insertions and deletions, a co-dominant STS marker of Vp-1B gene was developed and designated as Vp1B3, which in most cases could amplify either 845 or 569-bp fragment from the tolerant cultivars, and 652-bp from the susceptible ones. This Vp1B3 marker was mapped to chromosome 3BL using a set of Chinese Spring nulli-tetrasomic and ditelosomic lines. A total of 89 white-grained Chinese wheat cultivars and advanced lines, were used to validate the relationship between the polymorphic fragments of Vp1B3 and PHS tolerance. Statistical analysis indicated that Vp1B3 was strongly associated with PHS tolerance in this set of Chinese germplasm, suggesting that Vp1B3 could be used as an efficient and reliable co-dominant marker in the evaluation of wheat germplasm for PHS tolerance and marker-assisted breeding for PHS tolerant cultivars.

Back to PHS Main Page     Back to top