Potential and Pitfalls for Genomic Selection- Chad DechowDAIReXNET
Dr. Chad Dechow presented this information for DAIReXNET on Monday, January 14, 2013. For more information, please see our archived webinars page at www.extension.org/pages/15830/archived-dairy-cattle-webinars.
Marker Assisted Selection in Crop BreedingPawan Chauhan
Marker Assisted Selection is a value addition to conventional methods of Crop Breeding. It has been gaining importance in plant breeding with new generation of plant breeders and to get accurate and fast desired result from plant breeding.
Presentation delivered by Dr. Jesse Poland (Kansas State University, USA) at Borlaug Summit on Wheat for Food Security. March 25 - 28, 2014, Ciudad Obregon, Mexico.
http://www.borlaug100.org
I would like to share this presentation file.
Some basics information regarding to molecular plant breeding, hope this help the beginner who start working in this field.
Thanks for many original source of information (mainly from slideshare.net, IRRI, CIMMYT and any paper received from professor and some over the internet)
Balun design working at 5.8 GHz
The substrate is tsmc 0.18um.
This balun can be used for input and output matching.
Q factor is around 8 ( width of microstrip trace is 12.5 um).
Presentation by Dr. Sarah Cianférani-Sanglier, University of Strasbourg, Strasbourg, France. Talk given at Waters Antibody Drug Conjugates (ADC) 2014 Meeting, Nov. 20-21, Wilmslow UK.
Total workflow solutions that cater every budget, performance or throughput requirement for confirmatory dioxin analysis were discussed in the Thermo Scientific Lunch Seminar at the Dioxin 2014 conference. D. Hope, CEO & Owner Pacific Rim Laboratoris, presented about the economies of POPs analysis from the point of view of a leading laboratory using the very latest dioxin method kits. C. Cojocariu, Thermo Fisher Scientific, discussed recent changes in EU regulations which bring new opportunities for more labs to participate in dioxin analysis and about validating methods using Gas Chromatography triple quadrupole for PCDD/Fs with reference to the new EU Commission Regulation No. 709/2014.
use of DNA markers to select plants/animals with desirable traits,Phenotypic assessment and QTL analysis of herbage and seed production traits in perennial ryegrass
Genetic variation in GRIN genes encoding N-methyl-D-aspartate receptor (NMDAR) subunits has been associated with a spectrum of neurological and neuropsychiatric disorders. This talk will focus on clinical phenotype, functional consequences, and potential rescue pharmacology of disease-associated GRIN2D missense variants. The GRIN2D variants are located in the pre-M1 helix, agonist-binding domain, transmembrane domain M3, and the intracellular CTD. Developmental and epileptic encephalopathy (DEE) is the unifying phenotype across all 13 patients. The seizure types ranged from focal seizures, atypical absence seizures, tonic or atonic seizures, to epileptic spasms. Eight patients showed certain degree of hypotonia and movement disorders, three patients have autistic behavior and one patient showed symptoms of ADHD. Functional analysis in vitro on six novel GRIN2D variants reveals that that all six variants decreased receptor surface expression, which may underline certain shared clinical symptoms. Three variants (Leu670Phe, Ala675Thr, Ala678Asp) showed significantly enhanced agonist potency, and/or increased channel open probability, while the other three (Ser573Phe, Ser1271Phe, Arg1313Trp) presented reduced
sensitivity to endogenous protons and decreased channel open probability. Three variants (Ser573Phe, Ala675Thr, Ala678Asp) significantly decrease current amplitude. GluN2D-Leu670Phe
prolongs synaptic-like response time course and increases charge transfer. GluN2D-Ala678Asp transfection significantly reduced cell viability of cultured cortical neurons. In addition, a set of FDA-approved NMDAR channel blockers were evaluated for their ability to rescue functional changes of mutant receptors. This work suggests the importance of functional and biochemical validation for each individual variant. Rescue pharmacology in vitro may provide potential benefit of precision
medicine for a subset of severe pediatric neurodevelopmental diseases.
Potential and Pitfalls for Genomic Selection- Chad DechowDAIReXNET
Dr. Chad Dechow presented this information for DAIReXNET on Monday, January 14, 2013. For more information, please see our archived webinars page at www.extension.org/pages/15830/archived-dairy-cattle-webinars.
Marker Assisted Selection in Crop BreedingPawan Chauhan
Marker Assisted Selection is a value addition to conventional methods of Crop Breeding. It has been gaining importance in plant breeding with new generation of plant breeders and to get accurate and fast desired result from plant breeding.
Presentation delivered by Dr. Jesse Poland (Kansas State University, USA) at Borlaug Summit on Wheat for Food Security. March 25 - 28, 2014, Ciudad Obregon, Mexico.
http://www.borlaug100.org
I would like to share this presentation file.
Some basics information regarding to molecular plant breeding, hope this help the beginner who start working in this field.
Thanks for many original source of information (mainly from slideshare.net, IRRI, CIMMYT and any paper received from professor and some over the internet)
Balun design working at 5.8 GHz
The substrate is tsmc 0.18um.
This balun can be used for input and output matching.
Q factor is around 8 ( width of microstrip trace is 12.5 um).
Presentation by Dr. Sarah Cianférani-Sanglier, University of Strasbourg, Strasbourg, France. Talk given at Waters Antibody Drug Conjugates (ADC) 2014 Meeting, Nov. 20-21, Wilmslow UK.
Total workflow solutions that cater every budget, performance or throughput requirement for confirmatory dioxin analysis were discussed in the Thermo Scientific Lunch Seminar at the Dioxin 2014 conference. D. Hope, CEO & Owner Pacific Rim Laboratoris, presented about the economies of POPs analysis from the point of view of a leading laboratory using the very latest dioxin method kits. C. Cojocariu, Thermo Fisher Scientific, discussed recent changes in EU regulations which bring new opportunities for more labs to participate in dioxin analysis and about validating methods using Gas Chromatography triple quadrupole for PCDD/Fs with reference to the new EU Commission Regulation No. 709/2014.
use of DNA markers to select plants/animals with desirable traits,Phenotypic assessment and QTL analysis of herbage and seed production traits in perennial ryegrass
Genetic variation in GRIN genes encoding N-methyl-D-aspartate receptor (NMDAR) subunits has been associated with a spectrum of neurological and neuropsychiatric disorders. This talk will focus on clinical phenotype, functional consequences, and potential rescue pharmacology of disease-associated GRIN2D missense variants. The GRIN2D variants are located in the pre-M1 helix, agonist-binding domain, transmembrane domain M3, and the intracellular CTD. Developmental and epileptic encephalopathy (DEE) is the unifying phenotype across all 13 patients. The seizure types ranged from focal seizures, atypical absence seizures, tonic or atonic seizures, to epileptic spasms. Eight patients showed certain degree of hypotonia and movement disorders, three patients have autistic behavior and one patient showed symptoms of ADHD. Functional analysis in vitro on six novel GRIN2D variants reveals that that all six variants decreased receptor surface expression, which may underline certain shared clinical symptoms. Three variants (Leu670Phe, Ala675Thr, Ala678Asp) showed significantly enhanced agonist potency, and/or increased channel open probability, while the other three (Ser573Phe, Ser1271Phe, Arg1313Trp) presented reduced
sensitivity to endogenous protons and decreased channel open probability. Three variants (Ser573Phe, Ala675Thr, Ala678Asp) significantly decrease current amplitude. GluN2D-Leu670Phe
prolongs synaptic-like response time course and increases charge transfer. GluN2D-Ala678Asp transfection significantly reduced cell viability of cultured cortical neurons. In addition, a set of FDA-approved NMDAR channel blockers were evaluated for their ability to rescue functional changes of mutant receptors. This work suggests the importance of functional and biochemical validation for each individual variant. Rescue pharmacology in vitro may provide potential benefit of precision
medicine for a subset of severe pediatric neurodevelopmental diseases.
General conclusions
- Current methods used by the industry to evaluate protein quality are not capable of detecting existing differences among SBM
- The composition and the protein quality of SBM vary with the origin of the bean
- Different matrixes should be used for SBM of different origins, NIR technology might help
- Proteases might improve the uniformity and nutritive value of SBM batches
Transforming Maize-legume Value Chains –A Business Case for Climate-Smart Ag...CIMMYT
CIMMYT Senior Cropping Systems Agronomist Christian Thierfelder presented on climate-smart agriculture in southern Africa in a webinar titled Climate Resilient Agriculture Success Stories – Making a Case for Scale Up.
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
Macroeconomics- Movie Location
This will be used as part of your Personal Professional Portfolio once graded.
Objective:
Prepare a presentation or a paper using research, basic comparative analysis, data organization and application of economic information. You will make an informed assessment of an economic climate outside of the United States to accomplish an entertainment industry objective.
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
Francesca Gottschalk - How can education support child empowerment.pptxEduSkills OECD
Francesca Gottschalk from the OECD’s Centre for Educational Research and Innovation presents at the Ask an Expert Webinar: How can education support child empowerment?
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
A Strategic Approach: GenAI in EducationPeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
S4.3. Association Mapping, Breeder Ready markers and Genomic Selection
1. Association Mapping, Breeder Ready
markers and Genomic Selection
Raman Babu, Jill Cairns, Gary Atlin, PH Zaidi, Pichet Grudloyma, George
Mahuku, Sudha K Nair, Natalia Palacios, Pixley Kevin, Jose Crossa, BM
Prasanna and all the Breeders of CIMMYT
2. Outline
Association Mapping for Drought Tolerance – CIMMYT‟s
experience
● Are there large effect genes for GY_stress?
● Should we bother about “rare alleles” that have large
effects?
Association Mapping for Disease Resistance
Association Mapping (Candidate-gene based) for
Carotenoids
„Breeder-ready‟ markers for disease resistance and ProA
Integrating Genomic Selection in the breeding Pipeline
3. LD and Population structure
in DTMA-AM panel based on
55K SNPs
Average distance between two
markers is 55kb and Average EM-
R2 is 0.26
LD in DTMA panel is low and
hence suitable for association
mapping
Population structure is ‘mild’ and LaPosta Seq
association results were corrected DTP
for structure (through PCA) and
kinship by MLM
CIM-CALI
4. DTMA-AM panel and 55K SNPs can identify large
effect genes – 1. Grain Color
Psy1 92 – Yellow lines (1)
R² = 37%
186 – white lines (0)
SNP with largest significant association with
grain color located within one of the exons of
Phytoene Synthase1 (psy1) on chr.6
5. DTMA-AM panel and 55K SNPs can identify large
effect genes – 2. QPM 10 – QPM lines (1)
268 – Normal lines (0)
Opaque2
Ask2 at 7.01
R² = 8% R² = 16%
Besides opaque-2 and ask-2, several minor QTL regions
influencing kernel modification and tryptophan content
identified that overlap with previously reported regions…
6. Mapping Drought Tolerance
Strategy GWAS
AM-panel ~ 300 inbreds – TCd with CML312
Known DT sources La Posta Sequia C7; DTP C9, MBR etc.
Phenotyping 10 locations – Stress & Optimal
Heritabilities Kiboko-10-Late (0.64), M-10 –Tlalti (0.67), Thailand-
10 (0.49), M-Tlalti-09 (0.54), Zim-10 (0.22) Across
locations: 0.35
Phenotype used in Combined BLUPs of TC_GY under stress, corrected for
GWAS anthesis date
Genotyping Genome-wide, high density markers – 55K SNPs and GBS
markers (500K SNPs)
Statistical Model General Linear Model (PCA correction) and Mixed Linear
Model (PCA + Kinship – Q+K)
7. 12 -15 significant genomic regions identified for DT
7.0%
5.8%
5.7% 7.3%
5.7% 6.2%
5.5%
5.1%
5.1%
4.9%
Only 147 SNPs (~15 genomic regions) had R2 values more than 5%
8. Significant Genomic Regions associated with
TC_GY_Stress
Average GY of the stress trials – 1.3 t/ha
Heritability across locations – 0.32
Effect
SNP Chr Position P value MAF R2 (%) (kg/ha) Candidate Gene
SYN39332 10 142655119 9.62E-06 0.49 7.6 29.3 Starch Synthase
PZE-107042377 7 72216348 1.49E-05 0.32 7.3 35.6 Myb family transcription factor-related protein
PZE-108046876 8 77237318 2.33E-05 0.35 6.9 -34.4
PZE-110029252 10 50842298 7.77E-05 0.40 6.8 -26.3
PZE-107032355 7 45011599 6.62E-05 0.38 6.2 38.6
SYN37988 2 146399448 3.84E-05 0.26 6.1 49.5 TSA: Zea mays contig27975, mRNA sequence
PZE-101090321 1 80757998 1.67E-04 0.46 4.9 -31.4
PZE-109041733 9 62608362 1.35E-04 0.42 4.9 25.5
PZE-104047052 4 78536398 1.21E-04 0.32 4.7 30.1
9.
10. Rare Alleles with Large Effects
Average for Average for Average for
Marker Chr Position P Minor Allele MAF DD Dd dd Effect (kg/ha) DD Dd dd
PZE-104042524 4 67259441 3.70E-03 A 0.14 1499.5 1414.1 1382.8 116.6 7 59 188
PZE-101066401 1 49827350 1.54E-02 A 0.04 1487.8 1391.5 96.3 10 0 257
SYN36769 4 4914023 7.83E-03 A 0.06 1479.7 1355.9 1391.7 88.0 14 2 249
SYN26515 1 63053588 2.42E-03 A 0.06 1472.1 1253.0 1391.0 81.0 15 1 251
SYN1035 5 5786027 3.24E-02 G 0.07 1463.1 1395.2 1390.3 72.8 16 2 240
PZE-110053356 10 100124247 4.70E-03 A 0.11 1331.7 1381.2 1401.8 -70.1 17 24 224
PZE-104113536 4 194565443 7.31E-04 A 0.13 1334.7 1282.7 1405.3 -70.6 33 3 231
PZE-102096857 2 107898705 3.07E-03 G 0.08 1329.7 1400.4 -70.6 20 0 238
PZE-109074314 9 116545321 2.21E-04 G 0.08 1328.8 1400.3 -71.5 20 0 246
PZE-105127701 5 183968110 2.24E-04 A 0.07 1323.4 1400.7 -77.4 19 0 249
PZE-102121069 2 162773047 8.92E-04 G 0.06 1320.1 1400.2 -80.1 17 0 250
PZE-106064720 6 116886483 1.09E-02 A 0.07 1318.2 1307.6 1401.3 -83.1 17 1 248
SYN14434 2 15813081 1.40E-03 A 0.08 1314.6 1433.4 1398.6 -84.0 19 1 221
PZE-106056703 6 107499158 1.98E-04 G 0.06 1310.2 1307.6 1401.2 -91.0 15 1 251
SYN8914 3 194356323 4.25E-03 G 0.08 1307.9 1381.6 1400.1 -92.2 9 25 226
11. PZE-101066401
1
Rare Alleles with 49827350 SYN36769
4
GY 4914023
Positive Large A
POB.502 c3 F2 10-3-2-1-BBBBBB-B
(kg/ha)
1429.0 A
GY
(kg/ha)
[SYN-USAB2/SYN-ELIB2]-12-1-1-2-
Effects POB.502c3 F2 9-14-1-2-B-B-B-B
CLQ-RCYQ28=(CLQ6502*CLQ6601)-
1482.4 BBB 1497.3
[CML440/[[[K64R/G16SR]-39-1/[K64R/G16SR]-
20-2]-5-1-2-B*4/CML390]-B-39-2-B-4-#-1-
B-34-2-2-B*6-B 1476.1 B//ZM303c1-243-3-B-1-1-B]-9-1
PZE-104042524 DTPWC9-F24-4-3-1-B-B-B 1554.0 [[KILIMA ST94A]-30/MSV-03-1-10-B-
DTPWC9-F115-1-4-1-1-B-B-B 1483.4 1-B-B-1xP84c1 F27-4-1-6-B-5-B] F8-3-
4 2-2-1 x G16SeqC1F47-2-1-2-1-BBBB-
67259441 DTPWC9-F103-2-1-1-1-B-B-B 1469.6 B-xP84c1 F26-2-2-6-B-3-B]-3-1-
DTPYC9-F46-3-4-1-1-B-B-B 1535.9 B/CML395]-1-1 1419.5
GY [Pob.SEW-HG"B"c0F39-1-1-1-1xMBR
DTPYC9-F46-3-9-1-1-B-B 1461.7 C5 Bc F22-2-1-4-B-B-B-B-2-2-B-B-
A (kg/ha)
DTPYC9-F46-1-2-1-2-B-B 1606.1 B/CML442]-1-1 1333.2
90[SPMATC4/P500(SELY)]#-B-4-2-B-B 1483.8 DTPYC9-F13-2-1-1-2-B-B 1379.5
[Cuba/Guad C3 F34-2-1-1-B-B-B x
CML264Q]-1-1 1376.4
DTPYC9-F46-3-9-1-1-B-B 1461.7 CML-322 1428.5
La Posta Seq C7-F125-2-1-1-2-B-B-B 1436.8 SYN26515 DTPWC9-F115-1-4-1-1-B-B-B 1483.4
1 DTPWC9-F31-1-3-1-1-B-B-B 1492.0
La Posta Seq C7-F103-2-2-2-1-B-B-B 1626.9 DTPWC9-F67-1-2-1-2-B-B-B 1506.5
63053588
La Posta Seq C7-F180-3-1-1-1-B-B-B 1593.5 GY
DTPWC9-F104-5-4-1-1-B-B-B 1454.3
DTPYC9-F46-3-4-1-1-B-B-B 1535.9
La Posta Seq C7-F96-1-1-1-B-B 1482.1 A (kg/ha) DTPYC9-F46-3-9-1-1-B-B 1461.7
DTPYC9-F72-1-2-1-1-B-B 1411.4 CML444-B 1501.9 DTPYC9-F46-1-2-1-1-B-B 1552.7
S87P69Q(SIYF) 109-1-1-4-B 1518.4 DTPYC9-F46-1-2-1-2-B-B 1606.1
DTPWC9-F67-2-2-1-B-B-B 1568.7
CLQ-RCYQ40 = (CML165 x CLQ-6203)-B-
9-1-1-B*8 1509.3
CML497=[CL-00331*v]-3-B-3-2-1-B*6 1443.1
DTPWC9-F115-1-4-1-1-B-B-B 1483.4
DTPWC9-F109-2-6-1-1-B-B-B 1467.8
DTPWC9-F67-1-2-1-2-B-B-B 1506.5
DTPWC9-F104-5-4-1-1-B-B-B 1454.3
DTPWC9-F128-1-1-1-1-B-B-B 1390.9
DTPYC9-F143-5-4-1-2-B-B-B 1442.1
DTPYC9-F143-1-6-1-B-B 1414.6
DTPWC9-F67-2-2-1-B-B-B 1568.7
12. PZE-106056703 SYN14434
Rare Alleles with 6
107499158
2
15813081
Negative Large G
[CML444/CML395//DTPWC8F31-4-2-1-
6]-2-1-1-1-B*4 1331.949
A
P501SRc0-F2-47-3-2-1-B-B
[CML444/CML395//DTPWC8F31-1-1-2-2-
1268.038
Effects [(CML395/CML444)-B-4-1-3-1-
B/CML395//DTPWC8F31-1-1-2-2]-5-1-
BB]-4-2-2-2-2-BB-B
[CML444/CML395//DTPWC8F31-1-1-2-2-
1267.39
2-2-BB 1346.993 BB]-4-2-2-2-1-BB-B 1408.142
CML 384xMBR/MDR C3 Bc F58-2-1-3- 02SADVL2B-#-17-1-1-B 1419.196
SYN8914 B-B-B-B-3-1-B-B-BB-B 1344.688 [CML440/[[[K64R/G16SR]-39-1/[K64R/G16SR]-20-2]-
3 MBR C6 Bc F280-2-B-#-1-1-B-B-B-B-B- 5-1-2-B*4/CML390]-B-39-2-B-4-#-1-B//ZM303c1-243-
B 1256.056 3-B-1-1-B]-9-1
194356323
[G16SeqC1F47-2-1-2-1-BBBB-B-xP84c1 [CML144/[CML144/CML395]F2-5sx]-1-3-1-
G F27-4-1-6-B-5-B] F23-2-1-2-3 x P43C9- 3-B*4 1397.445
[CML198/ZSR923S4BULK-2-2-X-X-X-X-1- 1-1-1-1-1-BBBB-1-xP84c1 F26-2-2-6-B- [CML198/ZSR923S4BULK-2-2-X-X-X-X-1-
BB]-3-3-1-1-2-B*7 1196.562 3-B]-2-1-B/CML395]-1-1 1258.137 BB]-3-3-1-1-2-B*7 1196.562
S99TLWQ-B-8-1-B*5 1245.322 [M37W/ZM607#bF37sr-2-3sr-6-2-X]-8- [CML144/[CML144/CML395]F2-8sx]-1-1-1-
2-X-1-BB-B-xP84c1 F27-4-3-3-B-1-B] B*5 1171.759
4001 1292.372 F29-1-2-1-6 x [KILIMA ST94A]-30/MSV- [CML144/[CML144/CML395]F2-8sx]-1-2-3-
CLA41 1389.549 03-2-10-B-1-B-B-xP84c1 F27-4-1-6-B-5- 2-B*5 1203.073
(A.I.Z.T.V.C. 20-3-1-1-2-B-B x B]3-1-2-B/CML442]-1-1 1190.413 CLA222 1337.217
A.I.Z.T.V.C.PR93A-17-1-3-1-1-B-B)-B- [Pob.SEW-HG"B"c0F39-1-1-1-1xMBR [M37W/ZM607#bF37sr-2-3sr-6-2-X]-8-2-X-
C5 Bc F22-2-1-4-B-B-B-B-2-2-B-B- 1-BB-B-xP84c1 F27-4-3-3-B-1-B] F29-1-2-1-
14TL-1-3-B-B 1252.957 B/CML442]-1-1 1333.209 6 x [KILIMA ST94A]-30/MSV-03-2-10-B-1-B-
[G16SeqC1F47-2-1-2-1-BBBB-B-xP84c1 [MBR Et/MBR Bc C1 F4-1-1-3-B-B-B- B-xP84c1 F27-4-1-6-B-5-B]3-1-2-
F27-4-1-6-B-5-B] F23-1-3-1-1 x [KILIMA Bx1760B B1 Bco x Comp.-B-1-1-1-1-B- B/CML442]-1-1 1190.413
ST94A]-30/MSV-03-2-10-B-1-B-B- B-B/CML395]-1-1 1354.8 [Cuba/Guad C3 F34-2-1-1-B-B-B x
xP84c1 F27-4-1-6-B-5-B]-2-1- [CML 329/MBR C3 Am F103-1-1-2-B-B CML264Q]-1-1 1376.38
x CML486]-1-1 1346.293 CA00344 / PAC777F2-6-1-1-BB-B-B-BB 1321.875
B/CML395]-1-1 1270.448
[(87036/87923)-X-800-3-1-X-1-B-B-1-1- P44 C10MH8-30-4-B-4-1-B-B-B-B- 1329.436
POB.501c3 F2 13-8-2-1-BBBB 1383.065 1-B-B-xP84c1 F26-2-2-4-B-2-B] F47-3- P147-#136-5-1-B-1-BBB 1356.154
CL-RCY031=(CL-02410*CML-287)-B-9-1- 1-1-3 x M37W/ZM607#bF37sr-2-3sr-6- CLQ-6211=P62QC6HC13-1-3-BBB-6-B-7-6-
1-2-B*7 1433.411 2-X]-8-2-X-1-BB-B-xP84c1 F27-4-3-3-B- BBBB-7-9-B-B-B-B 1311.726
1-B]-3-2-B x P33c3 F64-1-1-4-BB]-1-1 1295.392 CML269=P25STEC1F13-6-1-1-#-BBB-f-##-
P390amC3/285x287 F73-3-2- B*6-B 1407.819
3xMIRTC5Am F96-1-1-1-3-1)-1-1-B 1399.776 CL-02143 P21C6S1MH247-5-B-1-1-2-BBB-
CL-G1837=G18SeqC2-F141-2-2-1-1-1- 1-##-B*10 1471.196
2-##-2-B*4 1275.469 CML421=P31DMR#1-55-2-3-2-1-B*18-B 1252.385
CML421=P31DMR#1-55-2-3-2-1-B*18- DTPWC9-F66-2-1-1-2-B-B-B 1291.755
B 1252.385
DTPWC9-F73-2-1-1-1-B-B-B 1329.332
13. Rare Alleles – Candidate genes
Candidate genes
Putative function
identified by Rare Alleles
upstream of a DNA biding/membrane
bound receptor Many membrane bound receptors like Rpk1, shown to confer DT in AT.
Less documented helicase domain proteins in AT proved for DT in CK
DEAD box Helicase domain dependent pathways
cross-talk between ethylene signalling and drought response pathways well-
related to ethyline insensitive2 documented
glyco poteins rich in hydroxy proline was first studied in Tracheophytes
Extensin like cell wall protein which can with stand severe stress
Annexin IV domain Role of Annexins in DT well-documented in AT
Peroxidase protein known for involvement in DT in rice, AT etc.
Major Facilitator Superfamily (MFS)
Transporters plays key roles in different stress conditions
over expression of Aspartate aminotransferase along with other
Aminotransferase genes has been patented for DT
CREB domain containing TF Known component in stress related pathways
Ubiquitin subgroup known component in drought tolerance pathways
14. Traits for which AM analysis accomplished in
DTMA-AM panel
GY_Stress_BLUPs
MSV
GLS
NDVI
Senescence
SPAD
Canopy senescence
ASI
Root traits (Shovelomics!)
Anaerobic Emergence
% reduction in shoot weight under waterlogged conditions
% reduction in root weight under water logged conditions
15. Following up the AM results
● BC-NILs for validation of important genomic
regions
● Identify MARS progenies with contrasting
genotypes and check the drought phenotypes
● Genotype the DH lines from DT x Normal
crosses and check the phenotypes
● Introgress validated genomic regions into tester
lines through MAS
16. Artesian – Recent Drought Tolerant
Hybrid from Syngenta
Base Hybrid Artesian Hybrid
17. Artesian – how was it developed?
Strategy Association mapping (candidate gene-based)
BC-MAS of 4-8 QTLs
DT source germplasm CML333, CML322, Cateto SP VII (Brazil), Confite Morocho AYA
38 (Peru), or Tuxpeno VEN 692 (Venezula)
AM-panel 575 inbreds – 47 different testers (mostly S-2 and S-3 TCHs)
Phenotyping 4 locations (Colorado, California and Chile) – Optimal & stress -
Yield reduction under stress was 40-60% from optimal
Genotyping 85 polymorphisms (corresponding to 57 candidate genes) and
149 random polymorphisms across 600 lines – in total only
~250 markers
Effect sizes of identified 60 to 650 kg/ha
genomic regions
Minimum P value of any 0.0001
significant region
18. Significant Conclusions – DT mapping
LD in DTMA-AM panel is low and hence conducive
for association mapping
55K genotype data is capable of identifying large
effect genes
„Reasonably large effect‟ genomic regions (10-15)
do exist for GY_Stress and co-locate with genes,
previously implicated for DT in At, rice and maize
9 genomic regions that had robust p-values
together explained 35% of phenotypic variance for
GY_Stress_Combined
Lines with multiple donor segments identified for
validation and introgression
19. Two Key genes in carotenoid biosynthetic pathway identified
Association Mapping
based on candidate
gene sequences
Lycopene epsilon cyclase (Harjes
et al. 2008; Science)
Hydroxylase (CrtRB-1/HydB-1)
(Yan et al. 2010; Nature Genetics)
20. Breeder-ready markers developed and routinely being used in the
H+ breeding program of CIMMYT for CrtRB1 and LcyE
AM leads to identification of
High
Key genes and polymorphisms ProvitA
+ + = maize!
MAS for MAS for
Deep orange LycE HydB
Polymorphisms validated in ears
diverse tropical genetic
backgrounds and breeder-ready
high throughput markers
developed
Routine use of markers and
selection of favorable
genotypes in H+ breeding
program
21. Allele Mining for CrtRB1 (HydB1) across various
Association Mapping Panels
Panel Genotypes with Fav. White(W)/Yellow(Y)
allele/Total
CIMMYT_Syngenta 24*/501 – 16 new sources All Yellow (Y)
CAM Panel
IMAS 16/430 (6 from ARC, SA and 14-W and 2-Y
3 from KARI)
Subtropical Collections 71/1131 – many new sources 24-W and 47-Y
ADP lines of 19/122 – “1” and 23/122 – “H”
SYNGENTA
PS: * out of 24, 8 were previously fixed for fav. allele of CrtRB1 in the H+ breeding
program through MAS
22. Association Mapping for Disease Resistance
MSV – Harare 2010 data (Heritability = 0.79) GLS-combined analysis (Heritability = 0.6)
23. MSV – Harare 2010 data (Heritability = 0.79)
Significant chromosomal regions (P < 1.0E-05) associated with MSV
resistance (Har-2010 data) based on DTMA-AM panel and 55K genotype
data (MLM)
Trait Trait
FDR (False Minor average average
Corr/Trend Corr/Trend discovery R2 Minor Allele Major for Minor for Major
Marker Chr Position P value Chi-square rate) (%) Allele Freq. Allele allele allele
PZE-101093951 1 86065123 4.50E-08 29.92 0.002 11.5 A 0.34 G 1.83 3.08
PZE-101098418 1 92204598 6.47E-07 24.77 0.011 9.5 G 0.36 A 2.15 2.95
SYN36281 1 187128850 1.93E-06 22.67 0.019 8.7 G 0.11 A 2.21 2.72
PZE-101094082 1 86384320 2.45E-06 22.21 0.020 8.5 G 0.39 A 1.99 3.10
PZE-104024779 4 28770811 4.04E-06 21.24 0.022 8.2 A 0.15 G 2.26 2.73
PZE-101098295 1 91837910 5.31E-06 20.72 0.022 8.0 A 0.33 G 2.12 2.92
PZE-108038832 8 59948253 5.57E-06 20.63 0.021 7.9 A 0.47 G 2.63 2.70
PZE-103070254 3 111066077 6.36E-06 20.38 0.022 7.8 G 0.24 A 3.07 2.52
PZE-101094056 1 86365447 6.37E-06 20.37 0.021 7.8 G 0.50 A 2.16 3.16
PZE-108039819 8 62905375 7.00E-06 20.19 0.022 7.8 G 0.46 A 2.62 2.69
PZE-101090488 1 80905706 7.02E-06 20.19 0.020 7.8 A 0.29 G 1.83 3.00
PZE-104016598 4 16339600 7.13E-06 20.16 0.019 7.8 A 0.33 C 2.21 2.87
PZE-102080891 2 64845534 7.21E-06 20.14 0.019 7.7 A 0.28 C 2.19 2.84
PZE-101098960 1 93244458 7.76E-06 20.00 0.019 7.7 A 0.40 G 3.11 2.36
24. Validation of AM regions and Breeder-ready markers for MSV
PZE01132220936
PHM14104_23
PZE0175698629
PZA00529_4
PZA02090_1
PZA03527_1
PZA02614_2
PZA03651_1
Candidate SNPs for MSV
Chr.1 Chr.3 Chr.4 Chr.8
Msv1 R R R PZE0186365075
csu1138_4
PZA00944_1
S S S PZE0195148805
PZE01101110579
PZE01111422982
R PZE0175698629
R S S PZE-101093951
S
R
S R S
S
R
S S R
S