Research Article

The Origin and Evolution of Tibetan Qingke Barley Based on Genome Sequencing Data  

Renxiang Cai1,2 , Jianhui Li1,2 , Jia Xu1,2
1 Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800,China
2 Cuixi Academy of Biotechnology, Zhuji, 311800,China
Author    Correspondence author
Triticeae Genomics and Genetics, 2019, Vol. 10, No. 1   doi: 10.5376/tgg.2019.10.0001
Received: 14 Nov., 2018    Accepted: 30 Jan., 2019    Published: 29 Mar., 2019
© 2019 BioPublisher Publishing Platform
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Cai R.X., Li J.H., and Xu J., 2019, The origin and evolution of Tibetan qingke barley based on genome sequencing data, Triticeae Genomics and Genetics, 10(1): 1-10 (doi: 10.5376/tgg.2019.10.0001)

Abstract

Tibetan Qingke barley is the main food of the Tibetans, which has been cultivated on the Qinghai-Tibet plateau for about 3 500 years. Tibetan Qingke barley is a variety of naked barley (Hordeum vulgare linn.var.nudum) belonging to the Hordeum of the family of Gramineae. With domestication and cultivation on the Qinghai-Tibet plateau for 3 500-4 000 years, it has been fully adapted to the extreme plateau climate. However, the origin and evolution of Tibetan Qingke barley has always been controversial at home and abroad. Tibetan Academy of Agriculture and Animal Husbandry, BGI and other research orgnizations made use of the genome sequencing data of 437 global barley germplasms including wild species, local varieties, and bred varieties to determine the origin and evolution of Tibetan Qingke barley through genetic analysis. The latest research showed that the Tibetan Qingke barley originated from the Eastern cultivated barley and entered southern Tibet through northern Pakistan, India and Nepal 3 500 years to 4 500 years ago. The low genetic diversity of Tibetan Qingke barley indicated that Tibet should be not the origin and evolution center of barley. Based on the haplotype of 5 major domestication genes of barley, it supported that six-row wild barley (H. agriocrithon) and Tibetan semi-wild barley originated from the wildification of cultivated barley or hybridization with wild barley, but did not support that the six-row wild barley (H. agriocrithon) is truly wild barley. Obviously, a large amount of sequencing data has answered the debate about the origin and evolution of the Tibetan Qingke barley at home and abroad.

Keywords
Tibetan Qingke barley; Hordeum; Origin; Evolution; Tibet

Tibetan Qingke barley is a variety of Hordeum (Hordeum vulgare linn.var.nudum). It has been cultivated on the Qinghai-Tibet Plateau for about 3 500 years and mainly distributed in Tibet, Qinghai, northwest Sichuan, southwest Gansu, and northwest Yunnan (Li et al., 2019).

 

Since the discovery of wild barley in 1938, scientists have found wild barley in various parts of the Qinghai-Tibet Plateau. Through the research, it is concluded that the Tibetan Qingke barley in the Qinghai-Tibet Plateau is actually the ancestor of barley in the Central Plains (Hsu, 1975; Dai et al., 2012). At the same time, Tibetan Qingke barley is one of the few wild and cultivated species in all food crops in the world (Hsu, 1975; Dequan and Tingwen, 1988). However, thousands of years later, people were surprised to find that found that when the altitude reached 4,200 m or more. And all the existing cultivars could not survive and only barley grass could grow.

 

As a variety of Hordeum, Tibetan Qingke barley can grow stubbornly at an altitude of 4 750 m, sheading and flowering, providing valuable food for Tibetans (Li et al., 2019). The famous Tibetan Qingke barley of Kongma, Gangba County, hides at the tip of the snow mountain and can grow at an altitude of 4 750 m. Only those who are destined to them can witness its dazzling brilliance. Tibetan Qingke barley in Gangba, because of its large germ, epidermis area and abundant beta-glucan, could be said as the "treasure" given by nature to human beings. It is known as the "rare species of Tibetan Qingke barley in the Himalayas region". But the Tibetan Qingke barley in Gangba also has its vulnerability. It can’t be duplicated and it will change or even disappear if it leave from its origin.

 

Barley may be one of the earliest evolved crops of human beings. Now most barley is used for animal fodder, malt, healthy food, and so on (Newman and Newman, 2006). Is Tibetan Qingke barley the same as barley? The origin and evolution of Tibetan Qingke barley has been controversial at home and abroad. At present, there are two main opinions: one is that Tibetan Qingke barley is considered to be evolved from the native wild barley in Tibet, i.e. Hordeum agriocrithon (H. agriocrithon); the other is that Tibetan Qingke barley originated from Fertile Crescent in West Asia (von Bothmer et al., 1990; Konishi, 2001; Tanno and Takeda, 2004).

 

Tibetan Qingke barley, where did it originate? Which is the way to Tibet? Is H. agriocrithon real wild barley? Is Tibet one of the origins and evolution center of barley? There has been controversy and no conclusion in the academic circles (Li et al., 2019).

 

1 Controversy of the Origin and Evolution of Tibetan Qingke Barley

There are two main views on the origin and evolution of Tibetan Qingke barley. One is the theory of Fertile Crescent migration spread, and the other is the theory of Tibetan origin and evolution. Fertile Crescent is universally accepted to be the origin and evolution center of barley and wheat over the world. Many western scholars believe that Tibetan Qingke barley is also a wheat from Fertile Crescent and is spread to Tibet and planted because of human migration.

 

Some Tibetan Qingke barley researchers of China generally believe that it evolved from Tibetan native wild barley, and Tibet is also one of the barley evolution centers in the world (Hsu, 1975; Dequan and Tingwen, 1988; Dai et al., 2012), which is based on the fact that Swedish botanist Aberg first discovered and reported the existence of six-rowed wild barley in Ganzi, Sichuan Province in 1938 (Åberg, 1938).

 

A group of Tibetan Qingke barley researchers from China also found six-rowed wild barley in many places of Tibet (Xu, 1982). Tibetan six-rowed wild barley has the same wild phenotype with the real wild barley (Hordeum vulgare ssp. Spontaneum, H. spontaneum) in Fertile Crescent is broken panicle (ears will split apart when ripened).

 

Besides, a variety of intermediate types of barley ranging from wild barley (two-rowed barley) to Tibetan Qingke barley (six-rowed barley), have also been found in Tibet, such as two-rowed naked barley and six-rowed barley, which many Tibetan Qingke barley researchers in China call Tibetan semi-wild barley (Hsu, 1975; Dequan and Tingwen, 1988).

 

However, the theory of Tibetan origin and evolution of Tibetan Qingke barley is doubted by many wheat researchers. First of all, the six-rowed wild barley and Tibetan semi-wild barley discovered exist as ruderals in highland barley field ridge rather than wild groups. Secondly, many studies have reported that the Tibetan six-rowed wild barley might be derived from the natural hybridization of wild barley and cultivated barley from Tibet (Konishi, 2001; Tanno and Takeda, 2004). Therefore, it is uncertain whether Tibetan six-rowed wild barley and Tibetan semi-wild barley are truly wild barley, which cannot fully support the hypothesis that Tibet is also the origin or evolution center of barley.

 

2 The Path of Barley into the Qinghai-Tibet Plateau

There are two main routes for barley from Fertile Crescent of west Asia to enter east Asia. The first one is to pass through the Inner Asia Mountain corridor, bypass the northern Qinghai-Tibet Plateau to the Loess Plateau, and then enter the northern and eastern China (blue dotted line, route 1) (Figure 1) (Li et al., 2007; Dong et al., 2015; Wang et al., 2016; Long et al., 2018). The second one is to pass through the Inner Asia Mountain corridor, bypass the northern Qinghai-Tibet Plateau and enter the Loess Plateau, continue to the south, reaching the northeast and southeast of the Qinghai-Tibet Plateau 4,000 years ago (yellow dotted line, route 2) (Figure 1) (Dong et al., 2015). There is abundant archaeological evidence to support it.

 

 

Figure 1 A possible route for barley to enter China (Adopted from (Zeng et al., 2018))

Note: Blue dotted line (route 1): the incoming route of barley in northern and eastern China; yellow dotted line (route 2): the incoming route from the Loess Plateau to the northeast of Tibet; pink dotted line (route 3): the research supports the incoming route from the southwestern part of Tibet

 

A third possible route of barley, supported by little archaeological information, is to spread eastward along the southern edge of the Tibetan Plateau (pink dotted line, route 3) (Figure 1). In the northeastern part of the Qinghai-Tibet Plateau, barley and wheat appeared with indigenous crops in China, such as sorghum and millet.When barley appeared in central and southeastern Tibet, it was accompanied by peas, rye, and flax originated from southwest Asian. In addition to millet originated from China (Guedes et al., 2014; Guedes et al., 2015), suggesting that it is possible that barley was introduced from the southwest of Qinghai-Tibet Plateau.

 

The recently discovered new archaeological relic of barley in northeastern India supports the hypothesis of the third possible route (Liu et al., 2017). The carbonized barley discovered is about 4 500 years old, earlier than previously reported remains from 4 000 to 3 500 years ago found in the northeastern Qinghai-Tibet Plateau (Dong et al., 2015).

 

Zeng et al. (2018) studied the relationship between the two geographical subgroups (through common ancestor coefficient analysis) of Tibetan Qingke barley and oriental barley, which were eastern-CA (middle and south Asia barley, samples from northern Pakistan, India and Nepal/western Qinghai-Tibet Plateau) and eastern-EA (east Asia barley, samples from eastern China and eastern Qinghai-Tibet Plateau). The research indicated that the D value (Tajima’s D) of eastern-CA was slightly higher than that of eastern-EA, which supported the hypothesis that barley was introduced from northern Pakistan, India, and Nepal to the southern Qinghai-Tibet Plateau (route 3, Figure 1).

 

Liu et al. (2017) found that the founder effect of Tibetan Qingke barley began about 4 500 years ago, which was close to that of the ancient barley in north-east India. Fu et al. (2000) considered that barley had reached southern Tibet about 3 500 years ago, and Zeng et al. (2018) speculated that the earliest time for barley to enter Tibet was 4 500 to 3 500 years ago.

 

Oriental cultivated barley was divided into two geographical subgroups by the Coancestry Coefficient analysis (Figure 2d), one from India and Nepal to Tibet (Figure 1, route 3), and became Tibetan Qingke barley after heavily cultivated as a staple food by Tibetans. The other reached north and east of China from northwest China (Figure 1, route 1), forming barley in northern and eastern China. Population history studies showed that the two branches were parted about 8,000 years ago (Figure 5c) (Zeng et al 2018).

 

 

Figure 2 Molecular and spatial polymorphisms of Vrs1 gene (from Zeng et al., 2018)

Notes: (a) The genetic structure of Vrs1, the golden triangle or diamond represented the same genotype as the reference gene sequence (Vrs1.b3), the green represented difference; (b) the Vrs1 haplotype network map based on SNP and InDel calculation; (c) haplotype distribution near the Vrs1 gene on barley genome 2H; (d) Geographical distribution of barley Vrs1 subtype


3 Tibet is not the Origin and Evolution Center of Barley

There have been many reports that Tibet is one of the origins and evolution centers of barley (Hsu, 1975; Dequan and Tingwen, 1988; Dai et al., 2012). Based on the results of PCA analysis, Tibetan Academy of Agriculture and Animal Husbandry and BGI divided the sequencing samples into four groups: wild barley, western barley, eastern barley, and Tibetan Qingke barley (Zeng et al., 2018). Through the population genetics analysis of nucleotide polymorphism (π), Watterson statistics (θW), gene diversity (HE), Tajima’s D, recombination rate (ρ), minor allele frequency (MAF), and linkage disequilibrium (LD), it was found that compared with wild barley, the π, θW and HE of western and eastern barley decreased by 50%, while Tibetan Qingke barley decreased by nearly 50% compared with those of western and eastern barley (Table 1). In addition, the SNP percentage of low frequency allele was the highest in wild species and the lowest in highland barley (Table 1). The LD of highland barley was the highest among all barley species, and the recombination rate ρ of Tibetan Qingke barley was about 16% of that of western barley and 50% of that of eastern barley (Zeng et al., 2018).

 

 

Table 1 Genetic diversity and Tajima’s D in barley groups (Adopted from Zeng et al., 2018)

Note: 1 WGS: Whole-genome sequencing; 2 Overlapped SNPs data: Whole-genome sequencing barley accessions overlapping SNP data with published exome sequences

 

It can be seen that compared with other barley species, Tibetan Qingke barley has the lowest genetic diversity, the lowest proportion of low-frequency allele SNP, the highest LD value, and the lowest recombination rate. The genetic information does not support Tibet as one of the origins and evolution centers of barley.

 

4 Tibetan Six-rowed Wild Barley and Tibetan Semi-wild Barley are not Real Wild Barley

Zeng et al. (2018) also analyzed the haplotypes of Tibetan six-rowed wild barley and Tibetan semi-wild barley on five evolved genes. On these genes, all the haplotypes of Tibetan six-rowed wild barley and Tibetan semi-wild barley belonged to cultivated barley type, not wild haplotype of wild barley, which indicated that Tibetan six-rowed wild barley and Tibetan semi-wild barley were not “pure” wild barley at least. In two materials of Tibetan semi-wild barley with brittle rachis, the researchers found that the brittle rachis was similar to the real wild barley in phenotypes (genotype was Btr1Btr2), in fact, was from the hybridization and recombination of two cultivated barley (genotypes were Btr1btr2 and btr1Btr2). The recombinant genotype was Btr1Btr2 with brittle rachis like wild barley. All of these evidences indicated that six-rowed wild barley and Tibetan semi-wild barley originated from cultivated barley feralization or natural hybridization between hybrid and wild barley.

 

5 Tibetan Qingke barley originates from the Barley in Fertile Crescent

Zeng et al. (2018) analyzed the haplotypes of five genes related to three main evolutionary traits of barley (including brittle rachis, two six-row and bare skin) to further explain the origin of Tibetan Qingke barley. Tibetan Qingke barley and other cultivated barley had the same haplotype at brittle rachis gene btr1, btr2 and two six-rowed gene int-c loci. The same 16 kb deletion on skin-naked nud genes was found in all Hulless barley materials, including Tibetan Qingke barley and two native varieties of Ethiopian Hulless barley.

 

In addition, on the other gene vrs1 controlling two six-row, except for 3 two-rowed Tibetan Qingke barley improved varieties (produced by crossing), 30% of other Tibetan Qingke barley carried vrs1.a1 subtype and 70% carried vrs1.a4 subtype (Figure 2b). A recent study found that the subtype vrs1.a4 might be originated from Uzbekistan in Central Asia. Therefore, a large number of vrs1.a4 existing in Tibetan Qingke barley population also supported that Tibetan Qingke barley was originated from Central Asia, that is, from the eastern barley (Figure 2d). The other subtypes of vrs1 were mutated in the exon region, resulting in the transformation of two-row to six-row. However, no mutations were detected in the ORF of vrs1 gene among vrs1.a4 subtypes. Compared with other subtypes of vrs1, the researchers found that a SNP variation occurring in the non-coding region was uniquely fixed in vrs1.a4, thus, this SNP might be the key variation of vrs1.a4 subtype to cause the change of the number of rows (Zeng et al., 2018).

 

To sum up, in the five evolutionary genes, Tibetan Qingke barley had exactly the same haplotype as cultivated barley in other parts of the world. This result supported that the barley all over the world originated from Fertile Crescent, while it did not support that the Tibetan Qingke barley originated from the Tibetan mainland.

 

6 The Relationship between Tibetan Qingke barley and Oriental Barley

6.1 Tibetan Qingke barley is more closely related to oriental barley

Zeng et al. (2018) defined most local varieties and improved varieties from west Asia, central Asia, Africa and Europe as western barley, and defined the local varieties from central Asia and east Asia (with the exception of Tibetan Qingke barley and Tibetan semi-wild barley) as eastern barley. A total of 1.55 M of SNPs (overlapped SNP for short) were detected in 177 copies of whole genome re-sequencing materials. With the overlapped SNP, the population structure of global barley material was analyzed, and all samples were classified as wild and cultivated type by the evolutionary tree and PCA (Figure 3a, Figure 3b). Cultivated barley was further divided into two branches that were geographically dependent (Figure 3c), with all western barley clustered in one branch, while eastern barley and Tibetan barley (Tibetan Qingke barley and Tibetan semi-wild barley) clustered in the other branch. The Tibetan Qingke barley was clustered with all the oriental barley, indicating that the relationship between Tibetan Qingke barley and oriental barley was closer (Zeng et al., 2018).

 

 

Figure 3 Evolutionary analysis and geographical distribution of barley germplasm resources based on SNP (Adopted from Zeng et al., 2018)

Notes: (a): evolutionary tree; (b): PCA analysis; (c): geographical distribution of different subgroups of barley; (d): coancestry coefficient, K=2 to K=9; the abbreviations in the picture are as follows: Hpu: H. pubiflorum; Hsp: wild barley H. spontaneum; Hag: six-rowed wild barley H. agriocrithon; TWB: Tibetan semi-wild barley

 

The coancestry coefficient between samples was further analyzed (Figure 3d). When K was 4-9, wild barley, western barley, and eastern barley populations were gradually divided into more subgroups. PCA analysis was performed separately for each type of barley, demonstrating the existence of these subpopulations. Samples from nearby geographic regions tended to cluster together to form subgroups, indicating that the differentiation of these subgroups was closely related to geographical sources (Morrell et al., 2014; Poets et al., 2015).

 

6.2 Tibetan Qingke barley is spread from the oriental cultivated barley

Zeng et al. (2018) used D statistics to study the relationship between Tibetan Qingke barley and other barley, and studied the relationship between Tibetan Qingke barley and wild barley, western barley and eastern barley (Figure 4a, b). The analysis of coancestry coefficient showed that wild barley was divided into two subgroups geographically and genetically, one in central Asia (wild-CA) and the other in west Asia (wild-WA). Tibetan Qingke barley was fixed to P3, P1, and P2, which were the full arrangement and combination of wild-CA, wild-WA, western barley, and eastern barley. When the eastern barley was fixed to P1, the D value obtained was the maximum. In addition, the distance between western barley and Tibet was much greater than that between wild-CA and Tibet geographically. However, the D value obtained by western barley (P1) was much higher than that obtained by wild-CA (P1), which showed that the Tibetan Qingke barley was not directly from the evolution of wild barley, but spread from the oriental cultivated barley.

 

 

Figure 4 Genetic relationship between Tibetan Qingke barley and other barleys (from Zeng et al., 2018)

Notes: (a) Geographical distribution of wild barley subpopulations; (b) D values calculated by the full permutation and combination of wild-WA, wild-CA, western barley, and oriental barley; (c) Geographical distribution of oriental barley subpopulations; (d) D values calculated by the full permutation and combination of wild barley, western barley, eastern-CA and eastern-EA (only listed a part); the abbreviations in the picture are as follows: wild-CA-Central Asian wild barley subgroup, wild-WA-West Asian wild barley subgroup, eastern-CA-Central-South Asian oriental cultivated barley subgroup, eastern-EA-East Asian oriental cultivated barley subgroup; (b, d) D statistics of 4 populations, the greater the D value, the closer the relationship between P1 and P3

 

7 Tibetan Qingke Barley——the Product of Founder Effect

The founder effect is a form of genetic drift that is determined by the genetic frequency of a few individuals in their offspring. It is an extreme genetic drift effect produced by a new population built up by a small number of individuals. Zeng and other researchers inferred that Tibetan Qingke barley had a founder effect in the history. Using barley WGS SNP to conduct a population history analysis of three populations of barley, the researchers found that compared with barley in eastern China and western bred varieties, the effective population size of Tibetan Qingke barley has decreased rapidly from 4500 years ago to 2500 years ago. This indicated that the event of founder effect occurred in the history of Tibetan Qingke barley which lasted for 2000 years (Figure 5b). During the same period, another branch of Central Asian barley bypassed the Qinghai-Tibet Plateau and entered the north and east of China through northwest China (Route 1, Figure 1). No change of population size occurred (Figure 5b), that is, there was no founder effect. This illustrated that the environment of Qinghai-Tibet Plateau may be the main factor in the occurrence of the founder effect (Zeng et al., 2018). Furthermore, the researchers speculated that the founder effect may also be caused by the following three situations: (1) A few individuals from eastern cultivated barley were introduced to Tibet and became Tibetan Qingke barley. (2) The terrain and environment of Tibet are changeable. Some barley was adapted to the local environment so it was regarded as the main local variety by the Tibetans and was artificially chosen to be preserved. (3) Tibetan Qingke barley is six-row naked barley, and barley includes those of two-row, six-row, skinned and naked. Only six-row naked barley (Tibetan Qingke barley) is widely cultivated in Tibet, which is also an artificial selection. All the above three factors are likely to cause the founder effect. Obviously, we can hold the idea that a small number of barley populations isolated from the original eastern barley population and cannot continue to communicate with the genes of the original population due to geographical isolation, climate adaptation, artificial selection and other factors. As a result, the gene frequencies of the two species were gradually separated, and finally a Tibetan Qingke barley population was formed.

 

 

Figure 5 Founder effect event of Tibetan Qingke barley (Adopted from Zeng et al., 2018)

Notes: (a) Distribution of genetic diversity of several groups of barley on chromosome 1H; (b) Changes in effective population of barley over time; (c) Separation time of Tibetan Qingke barley and local varieties in eastern China Biotechnology, Zhuji. Zhouying Wang, Bei Wang, Chunxia Zhuo and Yan Dong participated in the translation and proofread of the English version of the paper. The authors would like to express their sincere gratitude here

 

Authors’ contributions

LJH collected the references, revised and complemented the manuscript. XJ translated, revised and proofread the manuscript. FXJ designed the study, completed and revised the first draft, and finished the final version. All authors read and approved the final manuscript.

 

Acknowledgments

This study was granted by Cuixi Innovative Fund for Research and Development Project Funded by Cuixi Academy of Biotechnology, Zhuji. Zhouying Wang, Bei Wang, Chunxia Zhuo and Yan Dong participated in the translation and proofread of the English version of the paper. The authors would like to express their sincere gratitude here.

 

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https://doi.org/10.1038/s41467-018-07920-5
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Triticeae Genomics and Genetics
• Volume 10
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