Footprints of Selection Derived From Temporal Heterozygosity Patterns in a Barley Nested Association Mapping Population

Nowadays, genetic diversity more than ever represents a key driver of adaptation to climate challenges like drought, heat, and salinity. Therefore, there is a need to replenish the limited elite gene pools with favorable exotic alleles from the wild progenitors of our crops. Nested association mapping (NAM) populations represent one step toward exotic allele evaluation and enrichment of the elite gene pool. We investigated an adaptive selection strategy in the wild barley NAM population HEB-25 based on temporal genomic data by studying the fate of 214,979 SNP loci initially heterozygous in individual BC1S3 lines after five cycles of selfing and field propagation. We identified several loci exposed to adaptive selection in HEB-25. In total, 48.7% (104,725 SNPs) of initially heterozygous SNP calls in HEB-25 were fixed in BC1S3:8 generation, either toward the wild allele (19.9%) or the cultivated allele (28.8%). Most fixed SNP loci turned out to represent gene loci involved in domestication and flowering time as well as plant height, for example, btr1/btr2, thresh-1, Ppd-H1, and sdw1. Interestingly, also unknown loci were found where the exotic allele was fixed, hinting at potentially useful exotic alleles for plant breeding.

Download Full-text

Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

BMC Genomics ◽

10.1186/s12864-020-07258-7 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Bianca Büttner ◽

Vera Draba ◽

Klaus Pillen ◽

Günther Schweizer ◽

Andreas Maurer

Keyword(s):

Association Mapping ◽

Resistance Genes ◽

Genetic Basis ◽

Wild Barley ◽

Physical Map ◽

Resistance Qtls ◽

Nested Association Mapping ◽

Wild Allele ◽

Association Mapping Population ◽

Selection Of

Abstract Background Barley scald, caused by the fungus Rhynchosporium commune, is distributed worldwide to all barley growing areas especially in cool and humid climates. Scald is an economically important leaf disease resulting in yield losses of up to 40%. To breed resistant cultivars the identification of quantitative trait loci (QTLs) conferring resistance to scald is necessary. Introgressing promising resistance alleles of wild barley is a way to broaden the genetic basis of scald resistance in cultivated barley. Here, we apply nested association mapping (NAM) to map resistance QTLs in the barley NAM population HEB-25, comprising 1420 lines in BC1S3 generation, derived from crosses of 25 wild barley accessions with cv. Barke. Results In scald infection trials in the greenhouse variability of resistance across and within HEB-25 families was found. NAM based on 33,005 informative SNPs resulted in the identification of eight reliable QTLs for resistance against scald with most wild alleles increasing resistance as compared to cv. Barke. Three of them are located in the region of known resistance genes and two in the regions of QTLs, respectively. The most promising wild allele was found at Rrs17 in one specific wild donor. Also, novel QTLs with beneficial wild allele effects on scald resistance were detected. Conclusions To sum up, wild barley represents a rich resource for scald resistance. As the QTLs were linked to the physical map the identified candidate genes will facilitate cloning of the scald resistance genes. The closely linked flanking molecular markers can be used for marker-assisted selection of the respective resistance genes to integrate them in elite cultivars.

Download Full-text

Genomic Dissection of Peduncle Morphology in Barley through Nested Association Mapping

Plants ◽

10.3390/plants10010010 ◽

2020 ◽

Vol 10 (1) ◽

pp. 10

Author(s):

Sebastian Zahn ◽

Thomas Schmutzer ◽

Klaus Pillen ◽

Andreas Maurer

Keyword(s):

Quantitative Trait Loci ◽

Association Mapping ◽

Cross Section ◽

Quantitative Trait ◽

Spring Barley ◽

Raw Material ◽

Total Thickness ◽

Nested Association Mapping ◽

Elite Cultivar ◽

Major Qtl

Straw biomass and stability are crucial for stable yields. Moreover, straw harbors the potential to serve as a valuable raw material for bio-economic processes. The peduncle is the top part of the last shoot internode and carries the spike. This study investigates the genetic control of barley peduncle morphology. Therefore, 1411 BC1S3 lines of the nested association mapping (NAM) population “Halle Exotic Barley 25” (HEB-25), generated by crossing the spring barley elite cultivar Barke with an assortment of 25 exotic barley accessions, were used. Applying 50k Illumina Infinium iSelect SNP genotyping yielded new insights and a better understanding of the quantitative trait loci (QTL) involved in controlling the peduncle diameter traits, we found the total thickness of peduncle tissues and the area of the peduncle cross-section. We identified three major QTL regions on chromosomes 2H and 3H mainly impacting the traits. Remarkably, the exotic allele at the QTL on chromosome 3H improved all three traits investigated in this work. Introgressing this QTL in elite cultivars might facilitate to adjust peduncle morphology for improved plant stability or enlarged straw biomass production independent of flowering time and without detrimental effects on grain yield.

Download Full-text

Genetic Vulnerability and the Relationship of Commercial Germplasms of Maize in Brazil with the Nested Association Mapping Parents

PLoS ONE ◽

10.1371/journal.pone.0163739 ◽

2016 ◽

Vol 11 (10) ◽

pp. e0163739 ◽

Cited By ~ 2

Author(s):

Luciano Rogério Braatz de Andrade ◽

Roberto Fritsche Neto ◽

Ítalo Stefanine Correia Granato ◽

Gustavo César Sant’Ana ◽

Pedro Patric Pinho Morais ◽

...

Keyword(s):

Association Mapping ◽

Nested Association Mapping ◽

Genetic Vulnerability ◽

Relationship Of ◽

The Relationship

Download Full-text

Metabolomic Assessment of Key Maize Resources: GC-MS and NMR Profiling of Grain from B73 Hybrids of the Nested Association Mapping (NAM) Founders and of Geographically Diverse Landraces

Journal of Agricultural and Food Chemistry ◽

10.1021/acs.jafc.5b04901 ◽

2016 ◽

Vol 64 (10) ◽

pp. 2162-2172 ◽

Cited By ~ 17

Author(s):

Tyamagondlu V. Venkatesh ◽

Alexander W. Chassy ◽

Oliver Fiehn ◽

Sherry Flint-Garcia ◽

Qin Zeng ◽

...

Keyword(s):

Association Mapping ◽

Nested Association Mapping

Download Full-text

Latent Space Phenotyping: Automatic Image-Based Phenotyping for Treatment Studies

Plant Phenomics ◽

10.34133/2020/5801869 ◽

2020 ◽

Vol 2020 ◽

pp. 1-13 ◽

Cited By ~ 2

Author(s):

Jordan Ubbens ◽

Mikolaj Cieslak ◽

Przemyslaw Prusinkiewicz ◽

Isobel Parkin ◽

Jana Ebersbach ◽

...

Keyword(s):

Image Processing ◽

Association Mapping ◽

Stress Responses ◽

Interspecific Cross ◽

Response To Treatment ◽

Brassica Napus L ◽

Nested Association Mapping ◽

Latent Space ◽

Using Data ◽

Candidate Loci

Association mapping studies have enabled researchers to identify candidate loci for many important environmental tolerance factors, including agronomically relevant tolerance traits in plants. However, traditional genome-by-environment studies such as these require a phenotyping pipeline which is capable of accurately measuring stress responses, typically in an automated high-throughput context using image processing. In this work, we present Latent Space Phenotyping (LSP), a novel phenotyping method which is able to automatically detect and quantify response-to-treatment directly from images. We demonstrate example applications using data from an interspecific cross of the model C4 grass Setaria, a diversity panel of sorghum (S. bicolor), and the founder panel for a nested association mapping population of canola (Brassica napus L.). Using two synthetically generated image datasets, we then show that LSP is able to successfully recover the simulated QTL in both simple and complex synthetic imagery. We propose LSP as an alternative to traditional image analysis methods for phenotyping, enabling the phenotyping of arbitrary and potentially complex response traits without the need for engineering-complicated image-processing pipelines.

Download Full-text