Wheat breeding history reveals synergistic selection of pleiotropic genomic sites for plant architecture and grain yield

Li, Aili; Hao, Chenyang; Wang, Zhengyu; Geng, Shuaifeng; Jia, Meiling; Wang, Fang; Han, Xinyu; Kong, Xingchen; Yin, Lingjie; Shu, Tao; Deng, Zhongyin; Liao, Ruyi; Sun, Guoliang; Wang, Ke; Ye, Xingguo; Jiao, Chengzhi; Lü, Hongfeng; Zhou, Yun; Liu, Dengcai; Fu, Xiang‐Dong; Zhang, Xueyong; Mao, Long

doi:10.1016/j.molp.2022.01.004

Cited by 64 publications

(72 citation statements)

References 66 publications

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“…Biofortification has shown great potential for addressing micronutrient malnutrition in human populations ( White and Broadley, 2009 ). It has been widely recognized that biofortification strategy should focus on the staple food crops, such as wheat ( Triticum aestivum L.), which is a staple food for over 35% of the world’s population, and provides 20% of daily dietary protein, 21% of calories, and 14% of Cu, 11% of Zn, 13% of magnesium (Mg), and 15% of Fe ( Fan et al, 2008 ; Li et al, 2022 ). Wheat was found to contain relatively lower concentration of essential micronutrients (e.g., Fe, Zn, Cu, and Mn) in the grain ( Balint et al, 2001 ; Liu et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Did Wheat Breeding Simultaneously Alter Grain Concentrations of Macro- and Micro-Nutrient Over the Past 80 Years of Cultivar Releasing in China?

Hao

et al. 2022

Front. Plant Sci.

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Biofortification of wheat with mineral through crop breeding is a sustainable and cost-effective approach to address human mineral malnutrition. A better understanding of the trends of grain concentrations of mineral nutrients in wheat over the breeding period may help to assess the breeding progress to date. A 2-year field experiment using 138 Chinese wheat landraces and 154 cultivars was conducted. Grain concentrations of micronutrients (Cu and Mn) and macronutrients (N, P, and K) were measured and corrected for a yield level to elucidate the trends of these mineral nutrients over the 80 years of cultivar releasing and identify genetic variation for these mineral nutrients in cultivars and landraces. Large genetic variation exists for grain mineral nutrients concentrations among tested genotypes, indicating that selection for enhancing mineral nutrient concentrations in wheat is possible. Landraces showed a slightly wide genetic variation of grain Cu concentration and a much narrow variation of Mn concentration when compared to modern cultivars. Grain concentrations of Cu and Mn decreased slightly with increasing grain yield with a weak correlation, while N, P, and K concentrations declined obviously with increasing yield with a strong correlation, revealing that increased grain yield had a strong negative effect on grain concentration of macronutrients, but a relative weak negative effect on micronutrients concentrations. When considering the impact of the variation in yield on mineral concentrations, grain concentrations of Cu, Mn, N, P, and K in wheat cultivars released from 1933 to 2017 exhibited different trends with a year of variety release. Grain Cu, N, and P concentrations showed significant decreasing trends over a breeding period, while grain Mn and K concentrations showed no clear trend, suggesting wheat breeding in China over the past 80 years has decreased grain concentrations of Cu, N, and P, and did not alter Mn and K concentrations. Finally, a total of 14 outstanding accessions with high grain mineral nutrients concentrations/contents were identified, and these genotypes can be considered as promising donors for developing mineral-dense wheat cultivars.

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Section: Introductionmentioning

confidence: 99%

Did Wheat Breeding Simultaneously Alter Grain Concentrations of Macro- and Micro-Nutrient Over the Past 80 Years of Cultivar Releasing in China?

Hao

et al. 2022

Front. Plant Sci.

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“…From more than 23,090 wheat accessions stored in Chinese GeneBank that were collected across wheat growing regions in China, a mini-core collection of 262 Chinese wheat accessions, representing the genetic diversity of Chinese wheat, was constructed by phenotyping and SSR genotyping [ 4 ]. The collection consisted of 157 Chinese landraces (CL) and 105 cultivars, including 88 modern Chinese cultivars (MCC) and 17 introduced modern cultivars (IMC) [ 5 ]. Significant phenotypic differences were detected between CL and MCC [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

“…The collection consisted of 157 Chinese landraces (CL) and 105 cultivars, including 88 modern Chinese cultivars (MCC) and 17 introduced modern cultivars (IMC) [ 5 ]. Significant phenotypic differences were detected between CL and MCC [ 5 ]. Using SNP markers, 6.7% of the wheat genome was found to fall in selection sweeps between landraces and cultivars and genes known for yield improvement were identified using genome wide gene association study [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

“…Significant phenotypic differences were detected between CL and MCC [ 5 ]. Using SNP markers, 6.7% of the wheat genome was found to fall in selection sweeps between landraces and cultivars and genes known for yield improvement were identified using genome wide gene association study [ 5 ]. In plants, SNPs, rather than insertions/deletions (InDels), were commonly used to identify genomic variations that affect observable phenotypes.…”

Section: Introductionmentioning

confidence: 99%

“…Recently, 287 wheat accessions were used to identify 76,952 InDels. These InDels caused a frame shift in 2083 genes, including Ppd-D1 and GS5-1 and 182 rice homologs that have been functionally studied, demonstrating that InDels can impact on important functional genes [ 5 ]. The frequency of these frameshift InDels in modern cultivars (0.22) was significantly higher than that in landraces (0.17), suggesting that they were under artificial selection.…”

Section: Introductionmentioning

confidence: 99%

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InDels Identification and Association Analysis with Spike and Awn Length in Chinese Wheat Mini-Core Collection

Wang

Deng

Kong

et al. 2022

IJMS

Self Cite

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Diversity surveys of germplasm are important for gaining insight into the genomic basis for crop improvement; especially InDels, which are poorly understood in hexaploid common wheat. Here, we describe a map of 89,923 InDels from exome sequencing of 262 accessions of a Chinese wheat mini-core collection. Population structure analysis, principal component analysis and selective sweep analysis between landraces and cultivars were performed. Further genome-wide association study (GWAS) identified five QTL (Quantitative Trait Loci) that were associated with spike length, two of them, on chromosomes 2B and 6A, were detected in 10 phenotypic data sets. Assisted with RNA-seq data, we identified 14 and 21 genes, respectively that expressed in spike and rachis within the two QTL regions that can be further investigated for candidate genes discovery. Moreover, InDels were found to be associated with awn length on chromosomes 5A, 6B and 4A, which overlapped with previously reported genetic loci B1 (Tipped 1), B2 (Tipped 2) and Hd (Hooded). One of the genes TaAGL6 that was previously shown to affect floral organ development was found at the B2 locus to affect awn length development. Our study shows that trait-associated InDels may contribute to wheat improvement and may be valuable molecular markers for future wheat breeding

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Genome Sequence-Based Features of Wheat Genetic Diversity

Zhang,

Appels

2023

Compendium of Plant Genomes

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Common wheat is a hexaploid species crop that is widely recognized as an important staple food crop. The establishment of a gold standard reference genome sequences of the well-studied CHINESE SPRING, and its progenitors (including Triticum turgidum ssp. dicoccoides accession Zavitan, Triticum durum accession Svevo, Triticum urartu, Aegilops tauschii), in the last 5 years has dramatically promoted our understanding of wheat genome diversity and evolution through the resequencing of collections of wheat and its progenitors. In this chapter, we review progress in the analysis and interpretation of genome‑based studies of wheat focusing on geographic genome differentiation, interspecies gene flow, haplotype blocks, and gene diversity in breeding. We also consider approaches for efficiently discovering and integrating the genes and genome variations, hidden in Genebank collections, into wheat breeding programs.

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Wheat breeding history reveals synergistic selection of pleiotropic genomic sites for plant architecture and grain yield

Cited by 64 publications

References 66 publications

Did Wheat Breeding Simultaneously Alter Grain Concentrations of Macro- and Micro-Nutrient Over the Past 80 Years of Cultivar Releasing in China?

Did Wheat Breeding Simultaneously Alter Grain Concentrations of Macro- and Micro-Nutrient Over the Past 80 Years of Cultivar Releasing in China?

InDels Identification and Association Analysis with Spike and Awn Length in Chinese Wheat Mini-Core Collection

Genome Sequence-Based Features of Wheat Genetic Diversity

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