Increased Power To Dissect Adaptive Traits in Global Sorghum Diversity Using a Nested Association Mapping Population

Bouchet, Sophie; Olatoye, Marcus O.; Marla, Sandeep; Perumal, Ramasamy; Tesso, Tesfaye; Yu, Jianming; Tuinstra, Mitch; Morris, Geoffrey P.

doi:10.1534/genetics.116.198499

Cited by 157 publications

(192 citation statements)

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“…However, a significant knowledge gap exists in our understanding of mechanisms that operate in these species that can potentially help in adapting to a rapidly warming climate. Investigating vastly diverse sorghum accessions assembled from Asia, Africa, and the United States (Bouchet et al, ; Sunoj et al, ) and popular hybrids in controlled environments and field conditions, a highly conserved EMF mechanism was consistently documented (Figure ). To minimize heat stress‐induced increase in spikelet sterility in rice, Oryza officinalis , a wild rice, was used as a donor to introduce EMF trait into local popular rice varieties (Hirabayashi et al, ; Ishimaru et al, ), which are otherwise highly sensitive to heat stress at anthesis (Shi, Ishimaru, Gannaban, Oane, & Jagadish, ).…”

Section: Discussionmentioning

confidence: 99%

Deterioration of ovary plays a key role in heat stress‐induced spikelet sterility in sorghum

Chiluwal

Bheemanahalli

Kanaganahalli

et al. 2019

Plant Cell & Environment

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In sorghum (Sorghum bicolor [L.] Moench), the impact of heat stress during flowering on seed set is known, but mechanisms that lead to tolerance are not known. A diverse set of sorghum genotypes was tested under controlled environment and field conditions to ascertain the impact of heat stress on time‐of‐day of flowering, pollen viability, and ovarian tissue. A highly conserved early morning flowering was observed, wherein >90% of spikelets completed flowering within 30 min after dawn, both in inbreds and hybrids. A strong quantitative impact of heat stress was recorded before pollination (reduced pollen viability) and post pollination (reduced pollen tube growth and linear decline in fertility). Although viable pollen tube did reach the micropylar region, 100% spikelet sterility was recorded under 40/22°C (day/night temperatures), even in the tolerant genotype Macia. Heat stress induced significant damage to the ovarian tissue near the micropylar region, leading to highly condensed cytoplasmic contents and disintegrated nucleolus and nucleus in the susceptible genotype RTx430. Whereas, relatively less damages to ovarian cell organelles were observed in the tolerant genotype Macia under heat stress. Integrating higher tolerance in female reproductive organ will help in effective utilization of the early morning flowering mechanism to enhance sorghum productivity under current and future hotter climate.

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Section: Discussionmentioning

confidence: 99%

Deterioration of ovary plays a key role in heat stress‐induced spikelet sterility in sorghum

Chiluwal

Bheemanahalli

Kanaganahalli

et al. 2019

Plant Cell & Environment

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“…The population structure of the Senegalese sorghum landraces would be expected to increase spurious association and reduce the power of GWAS (Brachi, Morris, & Borevitz, 2011). Future studies with West African multi-parent mapping populations could breakup confounding LD and improve power to detect climate-adaptive loci (Bouchet et al, 2017;McMullen et al, 2009). Future studies with West African multi-parent mapping populations could breakup confounding LD and improve power to detect climate-adaptive loci (Bouchet et al, 2017;McMullen et al, 2009).…”

Section: Prospects For Genomic Dissection and Improvement Of Climatmentioning

confidence: 99%

Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal

Faye

Maina

et al. 2019

Ecology and Evolution

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Uncovering the genomic basis of climate adaptation in traditional crop varieties can provide insight into plant evolution and facilitate breeding for climate resilience. In the African cereal sorghum (Sorghum bicolor L. [Moench]), the genomic basis of adaptation to the semiarid Sahelian zone versus the subhumid Soudanian zone is largely unknown. To address this issue, we characterized a large panel of 421 georeferenced sorghum landrace accessions from Senegal and adjacent locations at 213,916 single‐nucleotide polymorphisms (SNPs) using genotyping‐by‐sequencing. Seven subpopulations distributed along the north‐south precipitation gradient were identified. Redundancy analysis found that climate variables explained up to 8% of SNP variation, with climate collinear with space explaining most of this variation (6%). Genome scans of nucleotide diversity suggest positive selection on chromosome 2, 4, 5, 7, and 10 in durra sorghums, with successive adaptation during diffusion along the Sahel. Putative selective sweeps were identified, several of which colocalize with stay‐green drought tolerance (Stg) loci, and a priori candidate genes for photoperiodic flowering and inflorescence morphology. Genome‐wide association studies of photoperiod sensitivity and panicle compactness identified 35 and 13 associations that colocalize with a priori candidate genes, respectively. Climate‐associated SNPs colocalize with Stg3a, Stg1, Stg2, and Ma6 and have allelic distribution consistent with adaptation across Sahelian and Soudanian zones. Taken together, the findings suggest an oligogenic basis of adaptation to Sahelian versus Soudanian climates, underpinned by variation in conserved floral regulatory pathways and other systems that are less understood in cereals.

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“…Conversely, nested association mapping (NAM) populations are produced by intercrossing one recurrent founder line with n other founder lines, which results in n recombinant inbred line (RIL) families that share the recurrent founder haplotype. The NAM design was developed in maize (McMullen et al ., ) and later applied to several maize genetic backgrounds (Bauer et al ., ) and different crops including soybean (Li et al ., ), sorghum (Bouchet et al ., ), barley (Maurer et al ., ; Nice et al ., ), and bread wheat (Bajgain et al ., ; Jordan et al ., ).…”

Section: Introductionmentioning

confidence: 99%

A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat

Kidane

Gesesse

Hailemariam

et al. 2019

Plant Biotechnology Journal

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Summary The Ethiopian plateau hosts thousands of durum wheat ( Triticum turgidum subsp. durum ) farmer varieties ( FV ) with high adaptability and breeding potential. To harness their unique allelic diversity, we produced a large nested association mapping ( NAM ) population intercrossing fifty Ethiopian FV s with an international elite durum wheat variety (Asassa). The Ethiopian NAM population (Et NAM ) is composed of fifty interconnected bi‐parental families, totalling 6280 recombinant inbred lines ( RIL s) that represent both a powerful quantitative trait loci ( QTL ) mapping tool, and a large pre‐breeding panel. Here, we discuss the molecular and phenotypic diversity of the Et NAM founder lines, then we use an array featuring 13 000 single nucleotide polymorphisms ( SNP s) to characterize a subset of 1200 Et NAM RIL s from 12 families. Finally, we test the usefulness of the population by mapping phenology traits and plant height using a genome wide association ( GWA ) approach. Et NAM RIL s showed high allelic variation and a genetic makeup combining genetic diversity from Ethiopian FV s with the international durum wheat allele pool. Et NAM SNP data were projected on the fully sequenced AB genome of wild emmer wheat, and were used to estimate pairwise linkage disequilibrium ( LD ) measures that reported an LD decay distance of 7.4 Mb on average, and balanced founder contributions across Et NAM families. GWA analyses identified 11 genomic loci individually affecting up to 3 days in flowering time and more than 1.6 cm in height. We argue that the Et NAM is a powerful tool to support the production of new durum wheat varieties targeting local and global agriculture.

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Increased Power To Dissect Adaptive Traits in Global Sorghum Diversity Using a Nested Association Mapping Population

Abstract: In crop species, adaptation to different agroclimatic regions creates useful variation but also leads to unwanted genetic correlations. Bouchet.......

Cited by 157 publications

References 87 publications

Deterioration of ovary plays a key role in heat stress‐induced spikelet sterility in sorghum

Deterioration of ovary plays a key role in heat stress‐induced spikelet sterility in sorghum

Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal

A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat

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