Direct introgression of untapped diversity into elite wheat lines

Singh, Sukhwinder; Jighly, Abdulqader; Sehgal, Deepmala; Burgueño, Juan; Joukhadar, Reem; Sharma, Achla; Vikram, Prashant; Sansaloni, Carolina; Govindan, Velu; Bhavani, Sridhar; Randhawa, M. S.; Solís-Moya, Ernesto; Pardo, Neftali; Arif, Mian Abdur Rehman; Laghari, K. A.; Basandrai, Daisy; Shokat, Sajid; Chaudhary, H. K.; Saeed, Nasir; Basandrai, Ashwani K.; Ledesma-Ramírez, Lourdes; Sohu, V. S.; Imtiaz, Muhammad; Sial, Mahboob Ali; Wenzl, Peter; Singh, Gyanendra Pratap; Bains, N. S.

doi:10.1038/s43016-021-00380-z

Cited by 25 publications

(29 citation statements)

References 52 publications

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“…The 6D MTA uncovered is supported by an MTA for heat tolerance reported in (13, 22) nearby on 6D. Singh et al, 2018 (13) state that the 6D MTA overlapped with an Ae.…”

Section: Discussionmentioning

confidence: 73%

Exotic alleles contribute to heat tolerance in wheat under field conditions

Molero

Coombes

Joynson

et al. 2022

Preprint

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Global warming is one of the most significant threats to food security. With temperatures predicted to rise and extreme weather events becoming more common we must safeguard food production by developing crop varieties that are more tolerant to heat stress without compromising yield under favourable conditions. By evaluating 149 spring wheat lines in the field under yield potential and heat stressed conditions, we demonstrate how strategic integration of exotic material significantly increases yield under heat stress compared to elite lines, with no significant yield penalty under favourable conditions. Genome-wide association analysis revealed three marker trait associations, which together increase yield under heat stress by over 50% compared to lines without the advantageous alleles and was associated with approximately 2°C lower canopy temperature. We identified an Aegilops tauschii introgression underlying the most significant of these associations. By comparing overlapping recombination of this introgressed segment between lines, we identified a 1.49Mbp region of the introgression responsible for this association that increases yield under heat stress by 32.4%. The genes within this region were extracted from diverse Ae. tauschii genomes, revealing a novel Ae. tauschii MAPK gene, a SOC1 orthologue and a pair of type-B two-component response regulators. Incorporating these exotic alleles into breeding programmes could serve as a pre-emptive strategy to produce high yielding wheat cultivars that are resilient to the effects of future climate uncertainty with no yield penalty under favourable conditions.

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“…The 6D MTA uncovered is supported by an MTA for heat tolerance reported in (13, 22) nearby on 6D. Singh et al, 2018 (13) state that the 6D MTA overlapped with an Ae.…”

Section: Discussionmentioning

confidence: 73%

Exotic alleles contribute to heat tolerance in wheat under field conditions

Molero

Coombes

Joynson

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…In addition, genebank genomics have already demonstrated how ‘molecular passports’ create value in genebank management by providing precise knowledge that goes beyond the boundaries of classical descriptors 20 , 21 . Nevertheless, due to the scarcity of agriculture-relevant information available for PGR, breeders often end up randomly choosing PGR as parents in crosses: an untargeted approach with low return of investment 22 . Furthermore, the value of PGR for agriculture and breeding is always relative to what can be found in modern cultivars.…”

Section: Background and Summarymentioning

confidence: 99%

“…The lower outputs for two-way crosses could be attributed to the increased proportion of deleterious PGR background still present in them, which also indicates that a realistic use of PGR variation for pre-breeding is achieved through three-way crosses. In fact, three-way crossing schemes are already the main strategy to introduce PGR variation into large-scale global pre-breeding programs such as Seeds of Discovery 22 ( https://seedsofdiscovery.org/ ). Although none of the PGR-derived progenies was as competitive as the best check cultivar ‘Informer’ (released in 2018), among the 173 F 3:4 progenies whose PGR parents were selected based on breeding values, three (2%) and 15 (9%) had better yield performance than the best newest (‘LGCharacter’, released in 2020) and the locally most grown cultivar (‘RGTReform’, released in 2014), respectively.…”

Section: Technical Validationmentioning

confidence: 99%

Large-scale genotyping and phenotyping of a worldwide winter wheat genebank for its use in pre-breeding

et al. 2022

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Plant genetic resources (PGR) stored at genebanks are humanity’s crop diversity savings for the future. Information on PGR contrasted with modern cultivars is key to select PGR parents for pre-breeding. Genotyping-by-sequencing was performed for 7,745 winter wheat PGR samples from the German Federal ex situ genebank at IPK Gatersleben and for 325 modern cultivars. Whole-genome shotgun sequencing was carried out for 446 diverse PGR samples and 322 modern cultivars and lines. In 19 field trials, 7,683 PGR and 232 elite cultivars were characterized for resistance to yellow rust - one of the major threats to wheat worldwide. Yield breeding values of 707 PGR were estimated using hybrid crosses with 36 cultivars - an approach that reduces the lack of agronomic adaptation of PGR and provides better estimates of their contribution to yield breeding. Cross-validations support the interoperability between genomic and phenotypic data. The here presented data are a stepping stone to unlock the functional variation of PGR for European pre-breeding and are the basis for future breeding and research activities.

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“…In an extreme example involving a cross between an elite variety and an exotic wild relative, selection is bound to reconstitute the elite genome because of the higher probabilities of favorable alleles in the elite over exotic genomes (Gorjanc et al 2016). This phenomenon is observed in a large-scale crossing program involving groups of one exotic and two elite parents, in which the resulting lines lost approximately two-thirds of the expected exotic genome (Singh et al 2021). In this regard, the approach of Origin Specific Genomic Selection (OSGS) (Yang et al 2020) can be used to specifically target genomic regions outside of RALLY QSLs for selection.…”

Section: Selection History and Future Direction In Winter Wheat Breedingmentioning

confidence: 99%

Analysis of historical selection in winter wheat

et al. 2022

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Key Message Modeling of the distribution of allele frequency over year of variety release identifies major loci involved in historical breeding of winter wheat. Abstract Winter wheat is a major crop with a rich selection history in the modern era of crop breeding. Genetic gains across economically important traits like yield have been well characterized and are the major force driving its production. Winter wheat is also an excellent model for analyzing historical genetic selection. As a proof of concept, we analyze two major collections of winter wheat varieties that were bred in Western Europe from 1916 to 2010, namely the Triticeae Genome (TG) and WAGTAIL panels, which include 333 and 403 varieties, respectively. We develop and apply a selection mapping approach, Regression of Alleles on Years (RALLY), in these panels, as well as in simulated populations. RALLY maps loci under sustained historical selection by using a simple logistic model to regress allele counts on years of variety release. To control for drift-induced allele frequency change, we develop a hybrid approach of genomic control and delta control. Within the TG panel, we identify 22 significant RALLY quantitative selection loci (QSLs) and estimate the local heritabilities for 12 traits across these QSLs. By correlating predicted marker effects with RALLY regression estimates, we show that alleles whose frequencies have increased over time are heavily biased toward conferring positive yield effect, but negative effects in flowering time, lodging, plant height and grain protein content. Altogether, our results (1) demonstrate the use of RALLY to identify selected genomic regions while controlling for drift, and (2) reveal key patterns in the historical selection in winter wheat and guide its future breeding.

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Direct introgression of untapped diversity into elite wheat lines

Cited by 25 publications

References 52 publications

Exotic alleles contribute to heat tolerance in wheat under field conditions

Exotic alleles contribute to heat tolerance in wheat under field conditions

Large-scale genotyping and phenotyping of a worldwide winter wheat genebank for its use in pre-breeding

Analysis of historical selection in winter wheat

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