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Published online 1 March 2007
Published in Crop Sci 47:821-828 (2007)
© 2007 Crop Science Society of America
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Reduction of a Triticum monococcum Chromosome Segment Carrying the Softness Genes Pina and Pinb Translocated to Bread Wheat

Marcos Bonafedea,c, Lingrang Kongb, Gabriela Tranquillic, Herbert Ohmb and Jorge Dubcovskya,*

a Dep. of Plant Sciences, Univ. of California, Davis, CA 95616-8780
b Dep. of Agronomy, Purdue Univ., 915 W. State St., West Lafayette, IN 47907-2054
c current address: Instituto de Recursos Biológicos, INTA Castelar, (1712) Villa Udaondo, Buenos Aires, Argentina. M. Bonafede and L. Kong contributed equally to this work

* Corresponding author (jdubcovsky{at}ucdavis.edu).


   ABSTRACT
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 NOTES
 ABSTRACT
INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 REFERENCES
 
Endosperm texture, i.e., the hardness or softness of the grain, is an important trait because it determines many end-use properties of wheat (Triticum aestivum L.). It is primarily controlled by the puroindoline genes (Pina and Pinb) at the Hardness (Ha) locus, mapped on the short arm of chromosome 5D. The introgression of functional Pin genes from diploid wheat Triticum monococcum L. chromosome 5Am into hexaploid wheat resulted in softer grains, suggesting that this translocation might be useful for soft wheat breeders. However, the translocated segment includes a large portion of the 5Am short arm and may carry detrimental genes for agronomic performance. In this study we have generated a backcross (BC) population of 210 individuals where 5A-5Am homeologous recombination was induced by the ph1b mutation to recover individuals with a reduced translocated segment. A map of this region was constructed using specific sequence tagged site (STS) markers for the three T. monococcum Ha–related genes, the completely linked BGGP gene, three wheat ESTs (BG606847, BF474606, and BQ168958), and two microsatellite markers. Eight plants with recombination events between XBggp and the closest proximal locus BG606847 were identified. Of these, four have the desired T. monococcum allele at the Ha locus. These plants carry a 6.3-cM segment of T. monococcum chromatin proximal to the Ha locus. This germplasm, which will be publicly available, and the molecular markers developed in this study will be valuable tools for soft wheat breeding programs.

Abbreviations: BC, backcross • CAPS, cleavage amplification polymorphic sequence • CS, Chinese Spring • EST, expressed sequence tag • Ha, hardness locus • PCR, polymerase chain reaction • SKCS, single-kernel characterization system • STS, sequence tagged site.


   INTRODUCTION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 REFERENCES
 
BREAD WHEAT is one of the major food crops in the world and is used to manufacture different products that require specific grain characteristics. Grain endosperm texture or grain hardness is an important trait that determines the end-use quality of wheat (Pomeranz and Williams, 1990; Morris, 2002). Soft wheat kernels require less energy to mill and produce flour particles with less starch damage after grinding or milling than hard wheats. Since broken and damaged starch granules absorb more water, hard wheats are suitable for bread and other yeast-leavened foods, whereas soft wheats are more suitable for cookies, cakes, and pastries (Tippless et al., 1994).

Grain texture is a simply inherited character, largely controlled by the Ha locus (Symes, 1965), which was mapped on the short arm of chromosome 5D (Mattern et al., 1973; Law et al., 1978). Though this main locus is referred to as hardness, softness is in fact the dominant trait.

A starch surface–associated protein (relative mass = 15 kDa) was found at high levels in soft wheat and at relatively low levels in hard wheat (Greenwell and Schofield, 1986). This protein, referred to as friabilin, provided a biochemical way to distinguish between hard and soft wheats. Subsequent work showed that friabilin is a composite of related lipid-binding proteins including three polypeptides called puroindoline a (PINA), puroindoline b (PINB), and the grain softness protein family GSP-1, which includes GSP-1a, GSP-1b, and GSP-1c (Jolly et al., 1993; Gautier et al., 1994; Morris et al., 1994; Rahman et al., 1994; Oda and Schofield, 1997; Turner et al., 1999).

The puroindoline proteins are encoded by the Pina-D1 and Pinb-D1 genes present on the short arm of chromosome 5D, whereas the GSP-1 proteins are encoded by the Gsp-A1, Gsp-B1, and Gsp-D1 genes, located on the short arms of chromosomes 5A, 5B, and 5D, respectively. Since the Pina-D1, Pinb-D1, and Gsp-D1 genes were mapped completely linked to the Ha locus on chromosome 5D, all three genes were initially considered as candidates for the differences in grain texture (Dubcovsky and Dvorák, 1995; Jolly et al., 1996; Sourdille et al., 1996; Giroux and Morris, 1997; Tranquilli et al., 1999; Turnbull et al., 2003). However, evidence from mutants and transgenic wheat suggest that the puroindolines and not the GSP-1 proteins are responsible for the differences in texture. Mutations in either the Pina-D1 (null mutation) or Pinb-D1 (single-point mutations) genes result in hard textures (Giroux and Morris, 1997, 1998; Lillemo and Morris, 2000; Morris et al., 2001; Chen et al., 2005, 2006; Ram et al., 2005; Xia et al., 2005), whereas deletions of the GSP-1 genes result in no changes in texture (Tranquilli et al., 2002). In addition, expression of wild-type Pinb sequence in transgenic wheat complements the hard phenotype (Beecher et al., 2002).

Homeologous puroindoline genes on chromosomes 5A and 5B have not been observed in cultivated wheats. However these genes are present in the diploid donors of the A and B genomes, indicating that they have been deleted from those chromosomes after polyploidization. Modern cultivated wheats have functional Pina-D1 and Pinb-D1 genes only on chromosome 5D (Tranquilli et al., 2002; Gautier et al., 2000). The presence of functional Pin homologs in wheat-related species opens the possibility to extend the range of grain soft textures. The introgression of functional copies of puroindoline genes from diploid species into hexaploid wheat resulted in softer grains, suggesting that these resources might be useful for soft wheat breeders (Tranquilli et al., 2002; See et al., 2004). However, these studies used either complete chromosome substitution lines (See et al., 2004) or large translocations, involving most of the short arm of chromosome 5A (Tranquilli et al., 2002), limiting their usefulness in commercial breeding programs.

Alien chromosomes or chromosome segments do not recombine well with the wheat chromosomes because of the presence of the Ph1 locus, which ensures correct homologous pairing (Riley and Chapman, 1958). Even closely related chromosome segments, such as those from the Am genome of T. monococcum (2n = 2x = 14) and the A genome of polyploid wheat, recombine poorly (Dubcovsky et al., 1995; Luo et al., 1996, 2000). Consequently, translocated segments are transferred to progenies as large linkage blocks, limiting recombination in the translocated region. If genes with detrimental effects on agronomic characteristics were present in the large translocated segments, they would be difficult to separate from the Pin genes.

To overcome this limitation, we used a line carrying a deletion of the Ph1 gene (Sears, 1977) to induce homeologous recombination between a large segment of the short arm of chromosome 5Am and wheat chromosome 5A. The objective of this work was to produce lines with active Pina-Am1 and Pinb-Am1 within a short translocated T. monococcum chromosome segment that would be useful in soft wheat breeding programs.


   MATERIALS AND METHODS
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
RESULTS AND DISCUSSION
 REFERENCES
 
Plant Material
The Chinese Spring (CS) line carrying the ph1b mutation (Sears, 1977) was crossed with a CS 5A/5Am recombinant substitution line number 25 carrying a 40-cM translocated segment from T. monococcum (Luo et al., 2000) including the Ha locus (Pina-Am1, Pinb-Am1, and GSP-Am1). This line was provided by Dr. J. Dvorák and Dr. M.-C. Luo (University of California, Davis). Since both parents carry the wild Ha allele on chromosome 5D (Pina-D1a, Pinb-D1a), all lines included in this study have the same Pin alleles on chromosome 5D. The F1 plants were grown and self-pollinated. The resulting F2 progenies were screened with molecular markers to select individuals homozygous for the ph1b mutation (sequence-characterized amplified region marker Ph302.3 [Wang et al., 2002]), and heterozygous for the 5A/5Am translocation (simple sequence repeat [microsatellite] locus Xgwm154). A dominant STS marker specific for Pina-Am1 was developed to confirm the presence of the T. monococcum Ha locus (see next section and Table 1). Selected plants were backcrossed to CS, and 210 grains were obtained. These plants were characterized with molecular markers previously mapped on chromosome 5A.


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  		Table 1. Sequence tagged site primer names, sequences, and expected sizes.

 
DNA Analysis
Genomic DNA was isolated following the protocol of Hoisington et al. (1994). Parental lines were screened with 10 microsatellite markers previously mapped on the short arm of chromosome 5A (Somers et al., 2004). Polymorphic microsatellite markers were used to characterize the 210 BC1 plants using polymerase chain reaction (PCR) conditions described before (Röder et al., 1998). PCR amplifications were conducted in a PTC-100 Thermocycler (MJ Research, Inc., Waltham, MA) in a final reaction volume of 25 µL containing 1x standard PCR buffer, 3.0 mM MgCl2, 0.3 µM of each primer, 200 µM of each dNTP, 1 U of Taq DNA polymerase, and 60 ng of template DNA.

In addition to the microsatellite markers we developed sequence tagged site (STS) markers for Pina-Am1, Pinb-Am1, Gsp-Am1. These markers were validated in 75 F2 individuals derived from the cross CS (phph) x CS 5A/5Am. DNA analyses were correlated with values of hardness index determined by the single kernel characterization system (SKCS). An additional STS marker was designed for the BGGP gene, which is immediately adjacent to Gsp and distal to the Pin genes (Chantret et al., 2004). Finally, three STSs were designed from T. monococcum ESTs BQ168958 and BG606847 and common wheat EST BF474606 previously assigned to the most distal bins from homeologous group 5 physical maps (Linkiewicz et al., 2004). The relative order of the wheat ESTs within the bin was predicted from the order of the orthologous genes on rice chromosome 12 (Gramene, 2006). Database searches were done using BLAST (NCBI, 2006), and primers were designed with the Primer3 software (Rozen and Skaletsky, 2000).

For markers BF474606 and BQ168958, where the designed primers did not reveal size polymorphisms between CS and CS(5A/5Am), the PCR products of both parental lines were sequenced and cleavage polymorphic sites were identified. PCR products were purified from agarose gels with QIAGen QIAquick PCR Purification Kit (QIAGen, Inc., Valencia, CA) and sequenced in ABI 3730 Capillary Electrophoresis Genetic Analyzer (Applied Biosystems, Foster City, CA).

Primer sequences, expected sizes, and PCR conditions are listed in Table 1. PCR products for different markers were separated by electrophoresis in 6% nondenaturing polyacrylamide gels (19:1 acrylamide to bisacrylamide ratio), except for the BF474606 marker, which was separated on 3% agarose gel. Gels were stained with ethidium bromide and visualized with UV light. Map distances were calculated with the program MapMaker (Lander et al., 1987) using the Kosambi function (Kosambi, 1944).


   RESULTS AND DISCUSSION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
REFERENCES
 
Molecular markers for T. monococcum Ha Locus
To facilitate the introgression of the T. monococcum Ha locus (softer grain textures) into commercial soft wheat varieties, we developed genome-specific PCR markers for this locus. We first compared the sequences of the Pina and Pinb genes from T. monococcum with those from T. aestivum D genome (Fig. 1A and B ). For the tightly linked XGsp-1 locus the T. monococcum sequence was compared with those from the three genomes of hexaploid T. aestivum (Fig. 1C). Since the primers were designed in regions carrying mutations specific for the T. monococcum sequence, the resulting markers are dominant (Fig. 1). Fragments of 296 bp, 249 bp, and 323 bp were amplified by Pina-Am1, Pinb-Am1, and Gsp- Am1 primer combinations, respectively, only when the T. monococcum chromosome segment was present (Fig. 1).


Figure 1
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  		Figure 1. BLAST (NCBI, 2006) and ClustalX (Thompson et al., 1997) sequence alignment of nucleotide sequences from (A) TmPina5A (T. monococcum Pina-Am1) and TaPina5D (T. aestivum Pina-1), (B) TmPinb5A (T. monococcum Pinb-Am1) and TaPinb5D (T. aestivum Pinb-1), and (C) TmGsp5A (T. monococcum Gsp-Am1) and TaGsp5A, 5B, 5D (T. aestivum Gsp-1). Primer sequences for sequence tagged site markers Pina-Am1, Pinb-Am1, and Gsp-Am1 are in underlined bold type. Shaded letters in DNA sequences correspond to the point mutations/insertion between T. monococcum and T. aestivum. Gel lanes: 1, DNA ladder; 2, donor of soft-textured grain (CS-5Am); 3, Chinese Spring; 4–26, BCF1 segregating population; 27, DNA ladder. Arrows indicate the T. monococcum–specific bands.

 
BGGP Marker
The dominant Ha-related markers described above cannot differentiate between homozygous and heterozygous carriers of the T. monococcum chromosome segment, limiting their use in marker-assisted selection. Consequently, a high-throughput codominant marker was developed from the closely linked gene for β-1-3-galactosyl-O-glycosyl-glycoprotein (BGGP). This gene is distal and very close to Gsp-1 both in T. monococcum (1.8 kb, AY491681) and T. aestivum (2.1 kb, CR626929) (Chantret et al., 2004, 2005).

A 12-bp region (ATTTGTTTTCTT) found in the third intron was present in T. monococcum (both DV92 and G1777) and absent in T. aestivum (GenBank CR626929.1). The primers flanking this deletion are specific for the A genome as confirmed by the absence of PCR amplification product in the DNA of the N5AT5D nullitetrasomic line (Fig. 2A ). The specificity of this marker to trace the T. monococcum chromosome segment was also verified by analyzing a set of 34 U.S. wheat varieties from different market classes currently used as parents of 17 mapping populations (Wheat CAP, 2006). None of these varieties showed the T. monococcum 220-bp diagnostic band.


Figure 2
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  		Figure 2. (A) BGGP polymerase chain reaction (PCR) products showing the 12-bp-shorter product in T. aestivum relative to the T. monococcum deletion. (B) BQ168958 PCR fragment digested with AluI. (C) BF474606 PCR product digested with MseI (3% agarose gel). (D) BG606847 dominant marker.

 
In summary, this marker is codominant, does not require digestion by restriction enzymes, and can be easily visualized in agarose or vertical polyacrylamide gels, facilitating its use in high-throughput marker-assisted selection strategies.

Validation of the Ha Markers
No recombination events were found between the XBggp and the puroindoline genes in our BC lines. Seventy five F2 lines derived from the cross CS(5Am) x CS(ph1b ph1b) were genotyped and their grain texture was measured using a SKCS to confirm the linkage between these markers and the softer texture of the grain. All lines have a CS 5D Ha allele and therefore functional Pina-D1 and Pinb-D1 alleles. Consequently, segregation is observed only for the presence of the 5Am puroindoline genes.

The average SKCS values from the 20 lines homozygous for the presence of both the T. monococcum and T. aestivum puroindoline genes (38.6 ± 6.7) showed a 41% reduction in hardness relative to the 17 lines carrying only the T. aestivum puroindolines on chromosome 5D (65.6 ± 12.9). The 38 heterozygous lines showed intermediate values (46.5 ± 9.3), which are smaller than the midpoint between the two homozygous classes (52.1). The degree of dominance was d = –0.41 (d = [H – ((AA + BB)/2))]/[(AA – BB)/2]), indicating a predominantly additive effect with a slight dominance of the T. monococcum allele.

The observed reduction of hardness values associated with the presence of T. monococcum Ha locus confirmed previous observations (Tranquilli et al., 2002; See et al., 2004). These results can be explained by the addition of T. monococcum puroindoline proteins, which remain functional in the T. aestivum background. The role of puroindolines in reducing grain hardness has been demonstrated before in transgenic plants. Krishnamurthy and Giroux (2001) showed that rice, a hard-textured cereal, has softer kernels when transformed with wheat puroindolines. Similar results were obtained by complementation of hard-textured wheats (Beecher et al., 2002; Hogg et al., 2005).

Reduction of the T. monococcum 5AmS Chromosome Segment
Microsatellite Markers
To identify the recombinant BC1 lines with the shortest T. monococcum segment, it was necessary to identify polymorphic markers covering the 5AS arm. We first screened 10 microsatellite markers previously mapped on this chromosome arm and found polymorphisms for 6 of them (Xgwm154, Xbarc186, Xgwm205, Xgwm293, Xgwm304, and Xgwm415). Two of these microsatellite markers (Xgwm205 and Xgwm293) were mapped 18 cM apart and added to the map (Fig. 3A ). The closest one to the Ha locus was Xgwm205, which was located 44 cM from the XBggp locus (Fig. 3A).


Figure 3
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  		Figure 3. (A) Genetic map for the 5A/5Am recombinant arm, involving the Ha locus. Genetic distances are in cM; (B) Physical map of the collinear region in rice. The location of each marker in the rice physical map is indicated in parentheses (Gramene, 2006).

 
Since the segment identified by the microsatellite markers was still considerably long, we developed additional markers using the rice genome as a template to select markers in the targeted region.

STS Markers Development
We selected wheat ESTs mapped to the distal bins of the short arm of homeologous group 5 (Linkiewicz et al., 2004) and searched for the closest homologs in rice. Our first target was the T. monococcum EST BQ168958, corresponding to a rice gene located 740 kb proximal to BGGP on rice chromosome 12. The genome-specific primers used to develop a cleavage amplification polymorphic sequence (CAPS) marker for BQ168958 are indicated in Table 1. Digestion of the 194-bp PCR product with restriction enzyme AluI resulted in two fragments of 100 and 94 bp in T. monococcum and no digestion in CS (194 bp) (Fig. 2B). Locus BQ168958 was mapped on our BC1 population 8.7 cM distal from microsatellite locus Xgwm205. The segment delimited by XBggp and BQ168958 was still relatively large (36 cM), so we developed additional markers (Fig. 3A).

The second CAPS marker was developed from T. aestivum EST BF474606, which corresponded to a rice gene located 160 kb proximal to BGGP on rice chromosome 12. Genome-specific primers for BF474606 (Table 1) amplified a PCR product of 390 bp that after digestion with restriction enzyme MseI produced differential fragments of 390 bp in CS and of 370 bp in T. monococcum (Fig. 2 C). Locus BF474606 was mapped 26.5 cM distal to BQ168958 and 9.2 cM proximal to XBggp. Using this new marker we selected the 13 recombinant chromosomes with the shortest introgressed segments (Fig. 3).

To identify lines with recombinant chromosomes carrying smaller T. monococcum chromosome segments, we developed an STS marker based on T. monococcum EST BG606847, which corresponds to a gene located in rice chromosome 12 only 90 kb proximal to BGGP. Genome-specific primers for BG606847, detailed in Table 1, amplified a PCR product of 170 bp in T. monococcum, and there was no product in CS (Fig. 2D). This locus was mapped on our BC1 population 6.3 cM proximal to XBggp (Fig. 3A).

Map Construction and Comparison with Rice
In the absence of the Ph1 gene, recombination between the T. monococcum chromosomes and T. aestivum chromosomes occur at a similar frequency as recombination between T. aestivum chromosomes in the presence of the Ph1 gene, and therefore, genetic distances in both situations are similar (Dubcovsky et al., 1995). A similar result was observed in this population. The genetic distance of 18 cM between microsatellite markers Xgwm293 and Xgwm205 observed in our population was almost identical to the 17 cM reported in the Synthetic x Opata-BARC 5A map (Song et al., 2005).

The XBggp and the three EST loci were colinear with the orthologous sequences on rice chromosome 12 (Fig. 3B). This was an expected result, based on the overall colinearity between the short arms of wheat homeologous group 5 and rice chromosome 12 reported before (Sorrells et al., 2003; Linkiewicz et al., 2004). The genetic distances between these four wheat markers showed a good correlation (R = 0.994) with the physical distances between these markers in rice. Therefore, in this case the rice genomic sequence was an excellent tool to predict the order and distance of the wheat markers.

Selected Recombinant Lines for Breeding Purposes
In the presence of the Ph1 gene, the T. monococcum and T. aestivum chromosomes showed highly reduced recombination (Dubcovsky et al., 1995; Luo et al., 2000). Therefore, the T. monococcum chromosome segment is transmitted almost as a single linkage block, eliminating recombination within the translocated region. Consequently, the high-throughput codominant XBggp marker linked to the Pin genes should be sufficient for selecting the T. monococcum Ha allele. However, checking the final homozygous lines with the T. monococcum Pin markers is recommended as a confirmation of the transfer of the targeted allele.

Recombinant lines that have the shortest T. monococcum segment have a reduced probability of carrying undesirable linked genes and minimize the region of the chromosome that is locked out for additional recombination. Eight plants with recombination events between XBggp and the closest proximal locus BG606847 were identified. Of these, four have the desired T. monococcum allele at the Ha locus, but one of them was discarded because of the presence of an additional proximal segment of T. monococcum detected by microsatellite marker Xgwm293. In each of the selected lines we confirmed with molecular markers the presence of the T. monococcum Pina and Pinb genes.

The T. monococcum segment proximal to XBggp in the original translocation line extended beyond Xgwm293 (Fig. 3), indicating a genetic distance of more than 63 cM. The reduction of the T. monococcum segment proximal to XBggp to less than 6.3 cM represents a minimum 10-fold reduction of the genetic length of the alien segment. However, to estimate the total length of the T. monococcum segment it is necessary to add the segment between the Ha locus and the telomere. Although no markers distal to Ha were included here, previous studies have shown that Ha is only 1.4 cM proximal to the XNor locus, the most distal marker on chromosome arm 5AmS (Dubcovsky et al., 1996). By adding the Ha proximal and distal T. monococcum segments it is possible to estimate the total length of the 5Am translocated segment at approximately 8 cM.

Two of these selected plants have been self-pollinated to recover homozygous recombinant lines where the ph1b deletion is eliminated. Seeds from the homozygous lines will be increased and deposited in the National Small Grain Collection. This publicly available germplasm, together with the markers developed in this study, will be useful to increase the range of soft textures available to soft wheat breeding programs.


   ACKNOWLEDGMENTS
 
This project was supported by the National Research Initiative of USDA's Cooperative State Research, Education, and Extension Service, CAP grant number 2006-55606-16629, and by Argentine grants BID 1201/OC-AR PID 234 and PICTO 08-12948.


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 MATERIALS AND METHODS
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All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher.

Received for publication July 16, 2006.


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