Sea Wheatgrass Genome Project

Dissecting the sea wheatgrass genome to transfer biotic stress resistance and abiotic stress tolerance into wheat.

PD: Li, Wanlong (South Dakota State University, Brookings, SD)
Co-PD: Xu, Steven S. (USDA-ARS, Fargo, ND)
Co-PD: Langham, Marie A. C. (South Dakota State University, Brookings, SD)
Co-PD: Ma, Qin (South Dakota State University, Brookings, SD)

Wheat production is facing numerous challenges from biotic and abiotic stresses. Alien gene transfer has been an effective approach for wheat germplasm enhancement. Sea wheatgrass (SWG) is a distant relative of wheat and a relatively untapped source for wheat improvement. We have identified high tolerance to waterlogging, manganese toxicity, salinity, heat and low nitrogen and resistance to wheat streak mosaic virus (temperature-insensitive), Fusarium head blight and sawflies (due to solid stem) in SWG and developed a large number of SWG-derived populations.

To facilitate simultaneous discovery and transfer of quantitative trait loci (QTL) for biotic stress resistance and abiotic stress tolerance more efficiently, we propose to dissect the SWG genome with three objectives:

Develop a draft SWG genome assembly and genome-specific markers,
Dissect SWG chromosomes into RobTs and localize agriculturally important genes and QTL, and
Dissect SWG chromosome arms by homoeologous recombination and select sub-arm introgressions of biotic stress resistance and abiotic stress tolerance.

This project addresses the Program Area Priorities of A1141 and NIFA-Kansas Wheat Commission co-fund and will serve our long-term goal to broaden the wheat genetic basis and develop novel germplasm that will contribute to a more sustainable wheat industry.

We are a team of interdisciplinary expertise in cytogenetics, molecular genetics, genomics, bioinformatics, plant breeding and pathology, and have materials, technologies and resources in place as evidenced from strong preliminary results. We expect to deliver a complete package of novel germplasm and associated resources, tools and knowledge for breeding wheat tolerance to abiotic and biotic stress.

Sea Wheat Grass chromosome specific PCR markers generated from this study

Marker Name	Forward primer (5`-> 3`)	Reverse primer (5`-> 3`)	Homeologous Group
WL4503	TACAACAGCAACAGAAGTGT	AGACACAGCTCCTCATCAACG	7
WL4505	GTAAGCTGCTCTCACCTGCAT	GGCCCATAAACTGGAACCCT	7
WL4511	TGCCTACACAAAGATGGAAGC	GCTCTGCAATTCTGCTTGTT	3
WL4513	GCTGTTTGCATTCACTTGCT	TTGTGTGAGTTTATGTGTGTGTG	3
WL4515	AAGTTCTAGGGGCAAAAAGGA	CTACGGAGATGCCGATCAA	4
WL4517	ATCCAACTAATTTTGTAAGCGTTAGC	CTACGAGAGCAAGCAGGAGG	5
WL4523	GCAGAACCATCGCCATCTC	GGGAAGCGGACTCTAAAAGAA	4
WL4531	ATATGGAAGAATAACGAACAGCA	GGTTCGGATTGCAGGGTT	6
WL4533	ATATGGAAGAATAACGAACAGCA	GGGCCTTTATGAATTGGCT	6
WL4537	AGATTTGCACTAACACGGGAA	TCGTTCCCCTCGCTTGTAGT	5
WL4539	ATCCAGGGGGTAAGCAACA	GTGCTGAATCGGTGTGGTTT	4
WL4569	GAGGCAGCACATCTAAAACAGC	GCAGAGAGAAAACCAGCTTCA	1
WL4581	GCAGGGAGAAATCAAAGAGGAA	TCTAATAAACCGCACGCAAATA	1
WL4583	CAAAGAAAAAGCTATCACTGGGT	ATTTGCGTGGCTGGTGAA	1
WL4591	CTTGCCCCGTCGATTTAC	ATTGTTAATGGTGGATGAGAAAG	2
WL4593	TTAATGCTGGAAGACGCC	TTTCCTTTGCGGATAGCAGATAG	2
WL4619	GTTATGGGTGTCAGTGAGGTG	GTGAACATCGCTGGAATTGG	2
WL4623	GCGAATAACGGACATCACTAGC	GATCGAGGTCATGGTACACTTGG	7
WL4625	TATGGCTTCATTACCTGTGTTG	CTTTGTTCCCATCATTCTCCTTG	5
WL4627	ACTTGCTGGAAAAACAAGCGATA	GGGACTTTGTTTAGATTTCCAAC	5
WL4661	ATGCTGTGATCGGTTCGGT	TTTTTGGCACGAAACAAACT	4
WL4663	AATGCCTATGAAGACAGGGTAAA	GTTGTGTGGCAGTTGTCGTATAG	4
WL4665	CTTGAAACGGCCCCTACTTTTT	GCTTTTCATGTGCCTAGTTATTG	2
WL4830	TACCATCCAGCCTAACCGAC	CTGGCCCTCTCTATGCACAT	4
WL4832	GGGACGGTACTCCCTCTTCT	TCCAACGGATAGTTCCTGGT	3
WL4874	TAGCCACCAAAAACCTCTCG	GGGGGAGAAACATCAGAAGA	2
WL4880	TAGCACACCTACCACGGACA	GGCAAATAAGGCTGAGGTGA	2
WL4902	AGACCTTGCCGGAATCAAC	CAACCCACATTGCCTTCTCT	6
WL4904	TCTGGAGGCCCACTATTGC	GGTTCGCCAGTTTGCTCTT	6
WL4906	GTCACGCCACCAACCATAG	GGGTCCGATCACATTCACTT	7
WL4908	TTTGCCTCCCAACCATTTAC	ACAACCTCTGCTTCCCTCTG	1
WL4914	TCTTATCCGCACGTTACAGC	GATTTCCCAGGATGCAACAC	4
WL4918	ATCACGACTGAGAGGGGAAA	TTGGTGTGAGCTTGGTTTGA	6
WL4922	TTTTCTTGTTGCTGCGAGTG	GTCCCTTTCGTCACACCCTA	1
WL4930	CAACGGATTTCATCGAGTGT	GTGGTGTTCTTGCTCCCTCT	5
WL4934	TATCCCATTGTCACCACGAA	AGGCTGAGGGTTTGTACCAG	7
WL4938	CATTGCCATTCACAGCATTT	TAGGTTTCGCGGTGAGAATA	2
WL4940	AGAGTTTGGGGCTGAATCCT	TCCACCAAGGTCAGAACACA	3
WL4966	TTTATGCCCAATCTTGTGTTCAT	CCAAAGCCCTTCCTGCAA	1
WL4968	CGCGAATCGTCTTGCTGAAA	AGTCGAAGTTGCATTCCAGTG	2
WL4972	ACCATGAATCGGGCACAGTA	AGATCAGATTACACACCTGCAA	4
WL4974	ACAGCTTGGGTCCATTCTCT	GCTAGTCCACTTAATTCCACCA	5
WL4976	GACTCGTACAAACACCATCTGA	CTGTTCCTCACACCCCTCTA	6
WL5009	GTCGATGTTCAGCTGGCA	GACGAGGGTGGGGAAGTG	5
WL5031	AAGTCCCCATTCCTCAGCAT	TCGCCATCAAAACCCTCTAC	2
WL5033	AATCTCATGTGCGTGCAATG	CACAAAGCTTAACGTGTACTGT	4
WL5035	GGAAAGGCGTCGATGGATAC	GGTAGAGCTGTAGACCGTCG	4
WL5039	CTACTACGAGCGATTGGTGC	CTACTTTATTACCCGGCGCG	6
WL5041	GAATAGGGTTGGCGTCGTTC	TCTGGGTCTGAACTTGCACT	7
WL5043	GAGGGTGTGGTAGGCTTAGTAA	GCATAACAAAGCATCGTCTGT	7
WL5049	CCCACCCGTATCCATCCTC	GCCGAAGAGCAGGAAGGT	1
WL5057	AGTCCTCTTCCTCATGCCAG	GTCCGCCTAGCCTTCAGTT	3
WL5059	GGTAAGTTGGTAACCCTGTAAGT	CTCGTTCAAGGCCAGTATTTGA	4
WL5063	AGAAAAGCCACACACACACA	CGACCCAGAACGACACCAT	1
WL5065	GGACAGCAGGACACAAAGTAAG	TGTTCTTCATTTTACCCCAGTGA	1
WL5067	CCCTACACGCCTGTTTTGTC	TGCAGAGTCACAGCCTTACA	6
WL5071	CGTTTATGTGCTGGATCGGG	GGCCCAGCTTGTCATTTTGA	7
WL5073	GCTCATTCGCAAATTCACCG	GCAGACCGGCCAAATCAA	7
WL5079	TGTAAACACCTAACAACCGCT	AATGCGCCATACAACTCAGG	3
WL5081	TGAACTTGAAGTGGATGCTCA	AGGAACGAGACAACATCACATAT	3
WL5083	GACGGAGAGCGGAGTGTACC	TTTTGCTCCATACCATCCACCT	5
WL5085	TGGAATTACAAATGGATCGATGG	TCATTCAGAAAGCTTGGACAATA	5
WL5087	TGAACTGAAGAGTGCAGAGCAAG	CGAGCGTTCTTTGTATTTGATTT	1
WL5091	CATCTCATTATCACCACTGTTCG	GGGCCTGATGCTAATCTCTT	2
WL5093	GTCGGTTCCTTGATTGCGTC	AGTAAGATTTGACTGCGTGCA	3
WL5123	GTCCGCCACAACGTATGA	TCGAGACAACATTCAGCGAA	4
WL5125	AGCAGAAAGAGAGAGGTGAAGT	GAGCATCCTAGTCAAAGTAACCA	4
WL5127	ACAACATGAGATGCACAGCT	GACTGCGTTGGTGGCTATAC	3
WL5129	TCGAGCGAGCCTTACGATTC	GGGGCTGCAAACGTTCTTAA	3
WL5133	CGATACATAGCACCCTCCGT	CTTTGCTTAGCCAGGTCCAC	4
WL5135	ACCCGTAACGAACACTTGATG	CTCACCCGTTTCTGCGTC	3
WL5137	TTGTGGAATGATCAGTAAACGC	ACACACACCCCAATTCCTGT	5
WL5166	GCGATTGGTGCAAGTAAACT	TCATGTTCAGCCCAGATTAGC	1
WL5170	CCCTTCTTCGACCTACAGCT	GTGATCGACGGGGCTAGAG	5
WL5172	ATAACGCTAGAGACTCCGCC	GAGATCTACGCCACGACTGA	5
WL5174	GTGCAAGCGTCGGTGAATT	TGGTTTATTCGTTTTCAGCCGT	7
WL5312	CTGCTTGGTCGCTGTATGTC	CTCGATCAACCGCTTACCAC	6
WL5316	CAGAGCGACAGATTCAACGG	CTGGAGCCATTGAAGCAGTG	6
WL5337	GATCAGCCCTATCCAAGCAA	AGGTACAAGCAGCCTTAGTGT	7
WL5341	GCCGCTAACCATCCTCAACT	GCCTAGATGACCAGCCCTTA	7
WL5356	TAAGGTCAGGTTGGCTTCGG	TTCGTCGCGGCCCTAAAA	7
WL5358	GCAATCAGGTGTGGGTTTCC	AACTGAGCGAGCTGGATGAT	7
WL5384	TGGTTAGGGTCGTACTCACTG	CGACACGCACGTTATAGAGA	3
WL5388	GGAACACCCTTTCTTCAGTCC	TAGCTATGTGGGCCAAGGAA	3
WL5390	AGAAGATCGACCGCCACAA	GTCGCTGTTGTGCTACTCG	3
WL5392	ACGGGACACTCAATAGAACTGT	GTAAGCCCTAACCCGTTGC	3
WL5396	CCGAATCTGCTGCGAAATAATT	ACCCTTGTCCGTTTAGTTCAC	2
WL5400	CACAGGCAGACTCGCAATT	AGTCACACAGCTCAGTACCC	2
WL5406	TGCGCCCAGTGTATATAGCA	TGCATCTCCCACACTCATCA	1
WL5410	GCGTTTATTGAGCTTCCGGT	TTTTCCTCCGTTCCAGTGTT	1
WL5412	GCCTCTAGAAACTCCCCTCC	GTTTTGAATCGGGCAGCGAT	1
WL5414	ACCGGTTCACCCTTGGAAAA	TGGACTGAGAGGAAGTTCGG	1
WL5416	TCACCTGTTCACCCTTGGAA	TTTGCAGACGATGATTGGGG	1
WL5422	ACCGAATCCAAGCTGATCCT	CTCCTGTTCTGAGTTGGTGC	1
WL5428	CGCCATGTCTACGAAAGCAT	GCAGGCACACATACGATCTC	7
WL5430	TGACAGTGGCGGATCTAGAA	AAGACCCTATCGTGTGGCAG	1
WL5432	GATTTCCGCACTAACTCTTTGC	ACCAGTCATGTACAACCATCAA	1
WL5436	TGGGAATTAATGTGGGGCCT	CGCTCTAAATTTCCCACGGG	5
WL5438	ACCGTCTCACAGCATATGGT	TCGATACCCAGCATCTCCAT	5
WL5440	TAATGTTGGCTTGCATCCGG	ATGACCTCGGCTATGACTGG	5

Anchoring the SWG-specific markers to the D-genome chromosomes of Aegilops tauschii and the subgenome origin

The homeologous are indicated at the top of the maps, and the marker loci are indicated at the right of the maps, and their position on the D-genome chromosomes are indicated the black bars. The markers in green are positive for the J₁ genome, the markers in the blue are positive for the J₂ genome, and the markers in black are codominant for both the J₁ and J₂ genomes as assayed the wheat-SWG addition lines. The scale bar in the bottom corner indicates 50 Mb.

Anchoring the SWG-specific markers to the D-genome chromosomes of Aegilops tauschii

The markers in green are specific to the J1 genome, the markers in blue are specific to the J2 genome, and the markers in black are codominant for both the J1 and the J2 genomes as assayed in the wheat-SWG addition lines. The scale bar in the left bottom corner indicates 50 Mb.

Multi-color GISH analyses of wheat-SWG amphiploid and chromosome lines

a) Amphiploid 13G819, b) 3J1L RobT, c) DA1J1L, d) MA1J2, e) MA2J1, f) MA2J2 + 2J2L, g) MA3J1, h) MA3J2, i) DA4J1, j) MA4J2, k) MA5J1, l) MA5J2, m) DA6J1, n) MA6J2, o) DA7J1, and p) MA7J2. The J1-genome chromosomes were painted in green by biotin-labeled genomic DNA of Th. elongatum, the J2-genome chromosomes were painted in red by digoxigenin-labeled genomic DNA of D. villosum, and the wheat chromosomes were counterstained in blue or purple by DAPI. The scale bars indicate 10 µm.

Assigning traits to SWG chromosomes

a) Segregation of the solid stem (bottom) is associated by chromosome 3J1. b) Segregation of blue seed color (bottom) is associated with chromosome 4J1. c) WSMV resistance (right) is associated with chromosome 2J1. d) WL tolerance (right) is associated with chromosome 1J1.