August 2015, Volume 57 Issue 8, Pages 662每731.


Cover Caption: Breeding with Endemic Wheat Subspecies
Endemic wheat subspecies are useful germplasms for improving the yield and environmental adaptabilities of common wheat. In this issue, Gu et al. (pp. 688每697) report the development of four sets of introgression lines using Chinese endemic subspecies including Tibetan semi-wild wheat, Xinjiang wheat and Yunnan wheat as donors. These introgression lines have been used to improve agronomic traits of bread wheat and to map yield-related QTLs.

 

          Molecular Ecology and Evolution
A haplotype block associated with thousand-kernel weight on chromosome 5DS in common wheat (Triticum aestivum L.)
Author: Yuquan Wang, Chenyang Hao, Jun Zheng, Hongmei Ge, Yang Zhou, Zhengqiang Ma and Xueyong Zhang
Journal of Integrative Plant Biology 2015 57(8): 662每672
Published Online: October 15, 2014
DOI: 10.1111/jipb.12294
      
    

Spike number per unit area, number of grains per spike, and thousand-kernel weight (TKW) are important yield components for wheat (Triticum aestivum L.). TKW has the highest heritability among the three components. We validated 27 simple sequence repeat (SSR) loci associated with TKW in an F2:5 breeding population grown in four environments. A cfd78265bp marker on chromosome 5DS showed the strongest association with TKW and had a significantly positive effect on TKW compared to allele cfd78259bp, with mean increases of 5.17, 3.63, 4.11, and 5.16 g in the four environments. Markers cfd67 and cfd40 flanking cfd78 also showed significantly positive associations with TKW with increases of 5.11, 3.29, 4.31, and 4.50 g for cfd67205, and 4.98, 3.49, 4.06, and 4.84 g for cfd40187 compared with cfd67203 and cfd40190 in the four environments, respectively. A major quantitative trait locus for TKW spanning 2.94 cM on chromosome 5DS was detected by association mapping. Strong linkage disequilibrium (LD) (r2 > 0.2) was detected among the three linked markers, which formed three haplotype blocks in the F2:5 breeding population. Mean TKW differences between HapB-I and HapB-II were 5.80, 4.41, 4.02, and 5.06 g in the four environments, respectively. Moreover, significant LD was detected only between cfd78 and cfd67 and between cfd67 and cfd40 in a germplasm collection. This study provides a base for cloning genes related to TKW on chromosome 5DS.

 

Wang Y, Hao C, Zheng J, Ge H, Zhou Y, Ma Z, Zhang X (2015) A haplotype block associated with thousand-kernel weight on chromosome 5DS in common wheat (Triticum aestivum L.). J Integr Plant Biol 57: 662–672. doi: 10.1111/jipb.12294

Abstract (Browse 819)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Molecular evolution and species-specific expansion of the NAP members in plants
Author: Kai Fan, Hao Shen, Noreen Bibi, Feng Li, Shuna Yuan, Ming Wang and Xuede Wang
Journal of Integrative Plant Biology 2015 57(8): 673每687
Published Online: March 4, 2015
DOI: 10.1111/jipb.12344
      
    

The NAP (NAC-Like, Activated by AP3/PI) subfamily is one of the important plant-specific transcription factors, and controls many vital biological processes in plants. In the current study, 197 NAP proteins were identified from 31 vascular plants, but no NAP members were found in eight non-vascular plants. All NAP proteins were phylogenetically classified into two groups (NAP I and NAP II), and the origin time of the NAP I group might be relatively later than that of the NAP II group. Furthermore, species-specific gene duplications, caused by segmental duplication events, resulted in the expansion of the NAP subfamily after species-divergence. Different groups have different expansion rates, and the NAP group preference was found during the expansion in plants. Moreover, the expansion of NAP proteins may be related to the gain and loss of introns. Besides, functional divergence was limited after the gene duplication. Abscisic acid (ABA) might play an important role in leaf senescence, which is regulated by NAP subfamily. These results could lay an important foundation for expansion and evolutionary analysis of NAP subfamily in plants.

 

Fan K, Shen H, Bibi N, Li F, Yuan S, Wang M, Wang X (2015) Molecular evolution and species-specific expansion of the NAP members in plants. J Integr Plant Biol 57: 673–687 doi: 10.1111/jipb.12344

Abstract (Browse 662)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
The NAP subfamily in plants can be phylogenetically classified into two groups. Abscisic acid might play an important role in leaf senescence which is regulated by NAP subfamily. These results could lay an important foundation for expansion and evolutionary analysis of NAP subfamily in plants.
          Molecular Physiology
Development, identification and utilization of introgression lines using Chinese endemic and synthetic wheat as donors
Author: Liqing Gu, Bo Wei, Renchun Fan, Xu Jia, Xianping Wang and Xiangqi Zhang
Journal of Integrative Plant Biology 2015 57(8): 688每697
Published Online: December 26, 2014
DOI: 10.1111/jipb.12324
      
    

Chromosome segmental introgression lines (ILs) are an effective way to utilize germplasm resources in crops. To improve agronomic traits of wheat cultivar (Triticum aestivum) Shi 4185, four sets of ILs were developed. The donors were Chinese endemic subspecies accessions Yunnan wheat (T. aestivum ssp. yunnanense) YN3, Tibetan semi-wild wheat (T. aestivum ssp. tibetanum) XZ-ZM19450, and Xinjiang wheat (T. aestivum ssp. petropavlovskyi) XJ5, and synthetic wheat HC-XM1620 derived from a cross between T. durum acc. D67.2/P66.270 with Aegilops tauschii acc. 218. Totals of 356, 366, 445 and 457 simple sequence repeat (SSR) markers were polymorphic between Shi 4185 and YN3, XZ-ZM19450, XJ5 and HC-XM1620, respectively. In total, 991 ILs were identified, including 300 derived from YN3, covering 95% of the genome of Shi 4185, 218 from XZ-ZM19450 (79%), 279 from XJ5 (97%), and 194 from HC-ZX1620 (84%). The sizes and locations of each introgression were determined from a consensus SSR linkage map. Using the ILs, 11 putative quantitative trait loci (QTLs) were identified for plant height (PH), spike length (SL) and grain number per spike (GNS). Comparative analyses of 24 elite ILs with the parents revealed that the four donor parents could be important resources to improve wheat SL and GNS. Our work offers a case for utilizing endemic landraces for QTL mapping and improvement of wheat cultivars using introgression lines.

 

Gu L, Wei B, Fan R, Jia X, Wang X, Zhang X (2015) Development, identification and utilization of introgression lines using Chinese endemic and synthetic wheat as donors. J Integr Plant Biol 57: 688–697 doi: 10.1111/jipb.12324

Abstract (Browse 684)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
As donor parents, the Chinese endemic wheat subspecies, which are the valuable gene recourses in China, were used to develop introgression lines so as to improve the agronomic traits of the wheat cultivar Shi 4185 and map the yield-related QTLs.
Combinations of Hd2 and Hd4 genes determine rice adaptability to Heilongjiang Province, northern limit of China  
Author: Xiufeng Li, Huazhao Liu, Maoqing Wang, Hualong Liu, Xiaojie Tian, Wenjia Zhou, Tianxiao L邦, Zhenyu Wang, Chengcai Chu, Jun Fang and Qingyun Bu
Journal of Integrative Plant Biology 2015 57(8): 698每707
Published Online: December 30, 2014
DOI: 10.1111/jipb.12326
      
    

Heading date is a key trait in rice domestication and adaption, and a number of quantitative trait loci (QTLs) have been identified. The rice (Oryza sativa L.) cultivars in the Heilongjiang Province, the northernmost region of China, have to flower extremely early to fulfill their life cycle. However, the critical genes or different gene combinations controlling early flowering in this region have not been determined. QTL and candidate gene analysis revealed that Hd2/Ghd7.1/OsPRR37 plays a major role in controlling rice distribution in Heilongjiang. Further association analysis with a collection of rice cultivars demonstrated that another three major QTL genes (Hd4/Ghd7, Hd5/DTH8/Ghd8, and Hd1) also participate in regulating heading date under natural long day (LD) conditions. Hd2/Ghd7.1/OsPRR37 and Hd4/Ghd7 are two major QTLs and function additively. With the northward rice cultivation, the Hd2/Ghd7.1/OsPRR37 and Hd4/Ghd7 haplotypes became non-functional alleles. Hd1 might be non-functional in most Heilongjiang rice varieties, implying that recessive hd1 were selected during local rice breeding. Non-functional Hd5/DTH8/Ghd8 is very rare, but constitutes a potential target for breeding extremely early flowering cultivars. Our results indicated that diverse genetic combinations of Hd1, Hd2, Hd4, and Hd5 determined the different distribution of rice varieties in this northernmost province of China.

 

Li X, Liu H, Wang M, Liu H, Tian X, Zhou W, Lü T, Wang Z, Chu C, Fang J, Bu Q (2015) Combinations of Hd2 and Hd4 genes determine rice adaptability to Heilongjiang Province, northern limit of China. J Integr Plant Biol 57: 698–707 doi: 10.1111/jipb.12326

Abstract (Browse 1696)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Heilongjiang province, located in north limit of china, is the largest elite base of rice production in china. Rice varieties from south to north of Heilongjiang have to flower more and more early. We revealed HD2 and HD4 are two key genes which act additively to determine flowering time in Heilongjiang province.
          Plant-environmental Interactions
Arabidopsis ROOT HAIR DEFECTIVE3 is involved in nitrogen starvation-induced anthocyanin accumulation  
Author: Jing Wang, Yan Wang, Ju Yang, Chunli Ma, Ying Zhang, Ting Ge, Zhi Qi and Yan Kang
Journal of Integrative Plant Biology 2015 57(8): 708每721
Published Online: December 10, 2014
DOI: 10.1111/jipb.12320
      
    

Anthocyanin accumulation is a common phenomenon seen in plants under environmental stress. In this study, we identified a new allele of ROOT HAIR DEFECTIVE3 (RHD3) showing an anthocyanin overaccumulation phenotype under nitrogen starvation conditions. It is known that ethylene negatively regulates light- and sucrose-induced anthocyanin biosynthesis. We hypothesized that RHD3 achieves its negative effect on anthocyanin biosynthesis via an ethylene-regulating pathway. In support of this, similar to rhd3 mutants, the Arabidopsis ethylene signaling mutants etr1, ein2, and ein3/eil1 showed an anthocyanin overaccumulation phenotype under nitrogen starvation conditions. The ethylene precursor ACC strongly suppressed anthocyanin accumulation, dependent on ETR1, EIN2, EIN3/EIL1, and, partially, RHD3. In addition, inactivating RHD3 partially reversed the suppressive effect of ETO1 inactivation-evoked endogenous ethylene production on anthocyanin accumulation. The expression of nitrogen starvation-induced anthocyanin biosynthesis genes was negatively regulated by RHD3, but ethylene response genes were positively regulated by RHD3. Wild-type seedlings overexpressing RHD3 showed similar phenotypes to rhd3 mutants, indicating the existence of a fine-tuned relationship between gene expression and function. RHD3 was initially identified as a gene involved in root hair development. This study uncovered a new physiological function of RHD3 in nitrogen starvation-induced anthocyanin accumulation and ethylene homeostasis. [Correction added on 6 August 2015, after first online publication: “RND3” corrected to “RHD3”.]

 

Wang J, Wang Y, Yang J, Ma C, Zhang Y, Ge T, Qi Z, Kang Y (2015) Arabidopsis ROOT HAIR DEFECTIVE3 is involved in nitrogen starvation-induced anthocyanin accumulation. J Integr Plant Biol 57: 708–721 doi: 10.1111/jipb.12320

Abstract (Browse 922)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
We found a mutant showing anthocyanin overaccumulation phenotype under nitrogen starvation condition, was defective in root and root hair development. A combination of positional cloning and next generation mapping, we identified ROOT HAIR DEFECTIVE3 (RHD3) and found it achieves negative effect on the anthocyanin biosynthesis through participating in ethylene-regulating pathway.
Detection and fine-mapping of SC7 resistance genes via linkage and association analysis in soybean
Author: Honglang Yan, Hui Wang, Hao Cheng, Zhenbin Hu, Shanshan Chu, Guozheng Zhang and Deyue Yu
Journal of Integrative Plant Biology 2015 57(8): 722每729
Published Online: December 22, 2014
DOI: 10.1111/jipb.12323
      
    

Soybean mosaic virus (SMV) disease is one of the most serious and broadly distributed soybean (Glycine max (L.) Merr.) diseases. Here, we combine the advantages of association and linkage analysis to identify and fine-map the soybean genes associated with resistance to SMV strain SC7. A set of 191 soybean accessions from different geographic origins and 184 recombinant inbred lines (RILs) derived from Kefeng No.1 (resistant) × Nannong 1138-2 (susceptible) were used in this study. The SC7 resistance genes were previously mapped to a 2.65 Mb region on chromosome 2 and a 380 kb region on chromosome 13. Among 19 single nucleotide polymorphisms (SNPs) detected via association analysis in the study, the SNP BARC-021625-04157 was located in the 2.65 Mb region, and the SNP BARC-041671-08065 was located near the 380 kb region; three genes harboring the SNPs were probably related to SC7 resistance. The resistance gene associated with BARC-021625-04157 was then fine-mapped to a region of approximately 158 kb on chromosome 2 using 184 RILs. Among the 15 genes within this region, one NBS-LRR type gene, one HSP40 gene and one serine carboxypeptidase-type gene might be candidate SC7 resistance genes. These results will be useful for map-based cloning and marker-assisted selection in soybean breeding programs.

 

Yan H, Wang H, Cheng H, Hu Z, Chu S, Zhang G, Yu D (2015) Detection and fine-mapping of SC7 resistance genes via linkage and association analysis in soybean. J Integr Plant Biol 57: 722–729 doi: 10.1111/jipb.12323

Abstract (Browse 837)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
SMV is one of the most serious soybean diseases worldwide. A total of 19 SNPs associated with disease rate were identified via association analysis, and one of them was fine-mapped to an interval less than 200 kb using linkage analysis. Finally, three candidate genes were obtained within this region.
          Obituary
In memory of Professor Biao Ding (1960 – 2015)  
Author: Asuka Itaya, William J. Lucas, Yijun Qi, Feng Qu, Ying Wang, Xuehua Zhong and Chun-Ming Liu
Journal of Integrative Plant Biology 2015 57(8): 730每731
Published Online: July 15, 2015
DOI: 10.1111/jipb.12381
Abstract (Browse 611)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
 

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